diff --git a/cypress/e2e/ingestion/files-ui.cy.ts b/cypress/e2e/ingestion/files-ui.cy.ts
index 68e1d74d..443f3cfe 100644
--- a/cypress/e2e/ingestion/files-ui.cy.ts
+++ b/cypress/e2e/ingestion/files-ui.cy.ts
@@ -2,6 +2,7 @@
 /// <reference types="cypress" />
 
 import { byTestId, testIds } from '../../support/selectors';
+import { continuePastMissingNodeCoverageWarning } from '../../support/journey-helpers';
 
 describe('File Handling and Processing', () => {
   const nodeFile = 'AngularTesting_nodelist_withseqs_TN93_BS.csv';
@@ -9,6 +10,11 @@ describe('File Handling and Processing', () => {
   const linkFile = 'AngularTesting_Epi_linklist_BS.csv';
   const additionalNodeFile = compatibleNodeFile;
   const geoJSONLocationFile = 'map-node-locations.geojson';
+  const coverageNodeFile = 'missing-node-coverage-nodes.csv';
+  const coverageLinkFile = 'missing-node-coverage-links.csv';
+  const matchedCoverageNodeFile = 'missing-node-coverage-matched-nodes.csv';
+  const matchedCoverageLinkFile = 'missing-node-coverage-matched-links.csv';
+  const extraCoverageNodeFile = 'missing-node-coverage-extra-node.csv';
   const loadNodeFile = () => cy.loadFiles([{ name: nodeFile, datatype: 'node' }]);
 
   beforeEach(() => {
@@ -180,6 +186,7 @@ describe('File Handling and Processing', () => {
     cy.contains('#file-table .file-table-row', linkFile, { timeout: 20000 }).should('be.visible');
     cy.get('.runtime-error-banner').should('not.exist');
     cy.get('#launch').should('not.be.disabled').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.get('.lm_tab.lm_active', { timeout: 20000 }).should('contain.text', '2D Network');
   });
 
@@ -286,6 +293,7 @@ describe('File Handling and Processing', () => {
     ]);
 
     cy.get('#launch').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.get('.lm_tab.lm_active', { timeout: 20000 }).should('contain.text', '2D Network');
 
     cy.window().its('commonService.session.data.nodes').should('have.length.greaterThan', 0);
@@ -303,6 +311,110 @@ describe('File Handling and Processing', () => {
     });
   });
 
+  it('gates launch when imported node and topology identifiers do not match', () => {
+    cy.loadFiles([
+      { name: coverageNodeFile, datatype: 'node', field1: 'id' },
+      { name: coverageLinkFile, datatype: 'link', field1: 'source', field2: 'target' },
+    ]);
+
+    cy.get('#launch').click({ force: true });
+    cy.get(byTestId(testIds.filesMissingNodeCoverageDialog), { timeout: 10000 })
+      .should('be.visible')
+      .parents('.p-dialog')
+      .as('coverageDialog');
+
+    cy.get('@coverageDialog')
+      .find(byTestId(testIds.filesMissingNodeDataSection))
+      .should('contain.text', 'Missing node data (1)')
+      .and('contain.text', 'D');
+    cy.get('@coverageDialog')
+      .find(byTestId(testIds.filesMissingLinkInformationSection))
+      .should('contain.text', 'Missing link information (1)')
+      .and('contain.text', 'C');
+    cy.window().then((win: any) => {
+      expect(win.commonService.session.network.launched).to.equal(false);
+      expect(win.commonService.session.data.nodes).to.have.length(0);
+    });
+
+    cy.get('@coverageDialog')
+      .find(byTestId(testIds.filesMissingNodeCoverageCancel))
+      .click({ force: true });
+    cy.get(byTestId(testIds.filesMissingNodeCoverageDialog)).should('not.exist');
+    cy.get('.lm_tab.lm_active').should('contain.text', 'Files');
+    cy.window().then((win: any) => {
+      expect(win.commonService.session.network.launched).to.equal(false);
+      expect(win.commonService.session.files.map((file: any) => file.name)).to.include.members([
+        coverageNodeFile,
+        coverageLinkFile,
+      ]);
+    });
+
+    cy.get('#launch').click({ force: true });
+    cy.get(byTestId(testIds.filesMissingNodeCoverageDialog), { timeout: 10000 })
+      .should('be.visible')
+      .parents('.p-dialog')
+      .find(byTestId(testIds.filesMissingNodeCoverageContinue))
+      .click({ force: true });
+
+    cy.window({ timeout: 30000 })
+      .its('commonService.session.network.isFullyLoaded')
+      .should('be.true');
+    cy.get('.lm_tab.lm_active', { timeout: 20000 }).should('contain.text', '2D Network');
+  });
+
+  it('launches without a coverage dialog when explicit topology is absent or fully matched', () => {
+    cy.loadFiles([{ name: coverageNodeFile, datatype: 'node', field1: 'id' }]);
+    cy.get('#launch').click({ force: true });
+    cy.get(byTestId(testIds.filesMissingNodeCoverageDialog)).should('not.exist');
+    cy.window({ timeout: 30000 })
+      .its('commonService.session.network.isFullyLoaded')
+      .should('be.true');
+
+    cy.visit('/?skipEula=1&skipDemoSession=1');
+    cy.get('#fileDropRef', { timeout: 15000 }).should('exist');
+
+    cy.loadFiles([
+      { name: matchedCoverageNodeFile, datatype: 'node', field1: 'id' },
+      { name: matchedCoverageLinkFile, datatype: 'link', field1: 'source', field2: 'target' },
+    ]);
+    cy.get('#launch').click({ force: true });
+    cy.get(byTestId(testIds.filesMissingNodeCoverageDialog)).should('not.exist');
+    cy.window({ timeout: 30000 })
+      .its('commonService.session.network.isFullyLoaded')
+      .should('be.true');
+  });
+
+  it('cancels an update without replacing the currently processed network', () => {
+    cy.loadFiles([
+      { name: matchedCoverageNodeFile, datatype: 'node', field1: 'id' },
+      { name: matchedCoverageLinkFile, datatype: 'link', field1: 'source', field2: 'target' },
+    ]);
+    cy.get('#launch').click({ force: true });
+    cy.window({ timeout: 30000 })
+      .its('commonService.session.network.isFullyLoaded')
+      .should('be.true');
+
+    cy.get(byTestId(testIds.appFileMenuButton)).click({ force: true });
+    cy.contains('[role="menuitem"]', 'Add Data').click({ force: true });
+    cy.get('.lm_tab.lm_active', { timeout: 20000 }).should('contain.text', 'Files');
+    cy.loadFiles([{ name: extraCoverageNodeFile, datatype: 'node', field1: 'id' }]);
+
+    cy.get(byTestId(testIds.filesUpdateButton)).click({ force: true });
+    cy.get(byTestId(testIds.filesMissingNodeCoverageDialog), { timeout: 10000 })
+      .should('be.visible')
+      .parents('.p-dialog')
+      .find(byTestId(testIds.filesMissingNodeCoverageCancel))
+      .click({ force: true });
+
+    cy.window().then((win: any) => {
+      expect(win.commonService.session.network.launched).to.equal(true);
+      expect(win.commonService.session.data.nodes.map((node: any) => node._id).sort())
+        .to.deep.equal(['A', 'B']);
+      expect(win.commonService.session.files.map((file: any) => file.name))
+        .to.include(extraCoverageNodeFile);
+    });
+  });
+
   it('detects a GeoJSON location file, joins feature centers to nodes, and stores the layer', () => {
     cy.attach_files('#fileDropRef', [nodeFile, geoJSONLocationFile]);
 
@@ -351,6 +463,7 @@ describe('File Handling and Processing', () => {
     ]);
 
     cy.get('#launch').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.get('.lm_tab.lm_active', { timeout: 20000 }).should('contain.text', '2D Network');
 
     cy.get(byTestId(testIds.appFileMenuButton)).click({ force: true });
@@ -383,6 +496,7 @@ describe('File Handling and Processing', () => {
     ]);
 
     cy.get('#launch').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.window({ timeout: 30000 })
       .its('commonService.session.network.isFullyLoaded')
       .should('be.true');
@@ -410,6 +524,7 @@ describe('File Handling and Processing', () => {
 
     cy.loadFiles([{ name: linkFile, datatype: 'link' }]);
     cy.get('#launch').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.window({ timeout: 30000 })
       .its('commonService.session.network.isFullyLoaded')
       .should('be.true');
@@ -428,6 +543,7 @@ describe('File Handling and Processing', () => {
     ]);
 
     cy.get('#launch').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.window({ timeout: 30000 })
       .its('commonService.session.network.isFullyLoaded')
       .should('be.true');
@@ -449,6 +565,7 @@ describe('File Handling and Processing', () => {
       .find('.flaticon-delete-1')
       .click({ force: true });
     cy.get('#launch').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.window({ timeout: 30000 })
       .its('commonService.session.network.isFullyLoaded')
       .should('be.true');
@@ -461,6 +578,7 @@ describe('File Handling and Processing', () => {
 
     cy.loadFiles([{ name: compatibleNodeFile, datatype: 'node', field1: '_id', field2: 'seq' }]);
     cy.get('#launch').should('contain.text', 'Update').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.window({ timeout: 30000 })
       .its('commonService.session.network.isFullyLoaded')
       .should('be.true');
@@ -482,6 +600,7 @@ describe('File Handling and Processing', () => {
     ]);
 
     cy.get('#launch').click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.window({ timeout: 30000 })
       .its('commonService.session.network.isFullyLoaded')
       .should('be.true');
@@ -504,6 +623,7 @@ describe('File Handling and Processing', () => {
     cy.get('#launch-reset-settings', { timeout: 20000 })
       .should('exist')
       .click({ force: true });
+    continuePastMissingNodeCoverageWarning();
     cy.window({ timeout: 30000 })
       .its('commonService.session.network.isFullyLoaded')
       .should('be.true');
diff --git a/cypress/e2e/journeys/flows/bubble-direct-launch-uploaded.cy.ts b/cypress/e2e/journeys/flows/bubble-direct-launch-uploaded.cy.ts
index 7148ba1b..985ff943 100644
--- a/cypress/e2e/journeys/flows/bubble-direct-launch-uploaded.cy.ts
+++ b/cypress/e2e/journeys/flows/bubble-direct-launch-uploaded.cy.ts
@@ -6,6 +6,7 @@ import {
   applyPreLaunchFileSettings,
   assertBubbleReady,
   assertSessionAfterLaunchCounts,
+  continuePastMissingNodeCoverageWarning,
   ensurePreLaunchProfileSynced,
   visitAppAndAcceptEula,
 } from '../../../support/journey-helpers';
@@ -31,6 +32,7 @@ const launchProfileDirectToBubble = (profile: DatasetProfile): void => {
   applyPreLaunchFileSettings(profile);
   ensurePreLaunchProfileSynced(profile);
   cy.get('#launch', { timeout: 15000 }).should('not.be.disabled').click({ force: true });
+  continuePastMissingNodeCoverageWarning();
   cy.window({ timeout: 120000 })
     .its('commonService.session.network.isFullyLoaded')
     .should('equal', true);
diff --git a/cypress/e2e/journeys/flows/map-direct-launch-uploaded.cy.ts b/cypress/e2e/journeys/flows/map-direct-launch-uploaded.cy.ts
index 15716556..ee51a40d 100644
--- a/cypress/e2e/journeys/flows/map-direct-launch-uploaded.cy.ts
+++ b/cypress/e2e/journeys/flows/map-direct-launch-uploaded.cy.ts
@@ -7,6 +7,7 @@ import {
   assertMapReady,
   assertMapRenderedCounts,
   assertSessionAfterLaunchCounts,
+  continuePastMissingNodeCoverageWarning,
   ensurePreLaunchProfileSynced,
   openMapSettingsDialog,
   selectMapField,
@@ -33,6 +34,7 @@ const launchProfileDirectToMap = (profile: DatasetProfile): void => {
   useOfflineMapLayers({ surviveLaunchReset: true });
 
   cy.get('#launch', { timeout: 15000 }).should('not.be.disabled').click({ force: true });
+  continuePastMissingNodeCoverageWarning();
   cy.get('#loading-information', { timeout: 120000 }).should('not.exist');
   cy.window({ timeout: 120000 })
     .its('commonService.session.network.isFullyLoaded')
diff --git a/cypress/e2e/journeys/flows/twod-mixed-origin-coloring.cy.ts b/cypress/e2e/journeys/flows/twod-mixed-origin-coloring.cy.ts
index 211bc8aa..88cd722b 100644
--- a/cypress/e2e/journeys/flows/twod-mixed-origin-coloring.cy.ts
+++ b/cypress/e2e/journeys/flows/twod-mixed-origin-coloring.cy.ts
@@ -4,6 +4,7 @@ import { getProfile } from '../datasets/profile';
 import {
   applyPreLaunchFileSettings,
   assertAfterLaunchCounts,
+  continuePastMissingNodeCoverageWarning,
   ensurePreLaunchProfileSynced,
   ensureTwoDNetworkView,
   launchAndWaitForProcessing,
@@ -229,6 +230,7 @@ describe('Journey Flow - 2D mixed-origin link coloring', () => {
     } else {
       cy.get('[data-testid="files-update-button"]', { timeout: 20000 }).should('not.be.disabled').click({ force: true });
     }
+    continuePastMissingNodeCoverageWarning();
     waitForProcessingDialogToClear();
     ensureTwoDNetworkView();
   };
diff --git a/cypress/e2e/view-state/dashboard-layout-core.cy.ts b/cypress/e2e/view-state/dashboard-layout-core.cy.ts
index b88905b1..cb72b851 100644
--- a/cypress/e2e/view-state/dashboard-layout-core.cy.ts
+++ b/cypress/e2e/view-state/dashboard-layout-core.cy.ts
@@ -89,7 +89,11 @@ describe('Dashboard View State - Golden Layout mechanics', () => {
       });
     });
 
+    cy.window().then((win) => {
+      win.commonService.visuals.bubble.goldenLayoutComponentResize();
+    });
     closeDashboardTab('Bubble');
+    cy.wait(250);
     assertOpenDashboardTabs(['2D Network', 'Map', 'Table']);
 
     focusDashboardTab('2D Network');
diff --git a/cypress/e2e/view-state/heatmap-view.cy.ts b/cypress/e2e/view-state/heatmap-view.cy.ts
index 1615a52e..a54d83a8 100644
--- a/cypress/e2e/view-state/heatmap-view.cy.ts
+++ b/cypress/e2e/view-state/heatmap-view.cy.ts
@@ -81,7 +81,7 @@ const assertHeatmapColorbarFormat = (expectedPercentageFormat: boolean): void =>
 
 describe('Heatmap View', () => {
   beforeEach(() => {
-    visitAppAndAcceptEula({ skipDemoSession: false });
+    visitAppAndAcceptEula({ skipDemoSession: false, dismissWelcomeOverlay: true });
     cy.window({ timeout: 60000 })
       .its('commonService.session.network.isFullyLoaded')
       .should('equal', true);
diff --git a/cypress/e2e/view-state/map-view.cy.ts b/cypress/e2e/view-state/map-view.cy.ts
index 3499aa3a..12184bb3 100644
--- a/cypress/e2e/view-state/map-view.cy.ts
+++ b/cypress/e2e/view-state/map-view.cy.ts
@@ -611,7 +611,7 @@ describe('Map View', () => {
         }, end))
         container.dispatchEvent(mm1);
 
-        const me1 = new MouseEvent('mouseend', Object.assign({
+        const me1 = new MouseEvent('mouseup', Object.assign({
           bubbles: true, cancelable: true, composed: true,
           pointerId: 1, pointerType: 'mouse', isPrimary: true, button: 0
         }, end))
@@ -628,13 +628,13 @@ describe('Map View', () => {
       cy.get('#centerMapButton').click({ force: true });
       cy.wait(500);
 
-      cy.window().then((win: any) => {
+      cy.window().should((win: any) => {
         const lmap = win.commonService.visuals.gisMap.lmap;
         const c = lmap.getCenter();
         newCenter = { lat: c.lat, lng: c.lng };
-        const latDiff = Math.abs(newCenter.lat - initialCenter.lat);
-        const lngDiff = Math.abs(newCenter.lng - initialCenter.lng);
-        expect(latDiff < 0.05 && lngDiff < 0.05).to.equal(true);
+        const zoom = lmap.getZoom();
+        const pixelDiff = lmap.project(newCenter, zoom).distanceTo(lmap.project(initialCenter, zoom));
+        expect(pixelDiff, 'center difference in rendered map pixels').to.be.at.most(1.5);
       })
     });
 
diff --git a/cypress/e2e/view-state/timeline-epicurve-view.cy.ts b/cypress/e2e/view-state/timeline-epicurve-view.cy.ts
index 6bffec49..51ece2dc 100644
--- a/cypress/e2e/view-state/timeline-epicurve-view.cy.ts
+++ b/cypress/e2e/view-state/timeline-epicurve-view.cy.ts
@@ -1,3 +1,9 @@
+import {
+  goToEpiCurveView,
+  setGlobalLinkThreshold,
+  visitAppAndAcceptEula,
+} from '../../support/journey-helpers';
+
 describe('Epi Curve / Timeline View', () => {
     const selectors = {
       container: '#epiCurve',
@@ -6,15 +12,9 @@ describe('Epi Curve / Timeline View', () => {
     };
   
     beforeEach(() => {
-      cy.visit('/');
-      cy.wait(6000);
-  
-      cy.contains('button', 'Continue with Sample Dataset', { timeout: 10000 }).click({ force: true });
-      cy.get('#overlay').should('not.be.visible', { timeout: 10000 });
-  
-      cy.contains('button', 'View').click();
-      cy.contains('button[mat-menu-item]', 'Epi Curve').click();
-  
+      visitAppAndAcceptEula({ skipDemoSession: false, dismissWelcomeOverlay: true });
+      goToEpiCurveView();
+
       cy.get(selectors.container, { timeout: 15000 }).should('be.visible');
     });
   
@@ -129,24 +129,16 @@ describe('Epi Curve / Timeline View', () => {
 
         let expectedClusterCount = 2
         cy.contains('#global-settings-modal .nav-link', 'Filtering').click();
-        for (let i = 0; i < 6; i++) {
-          cy.get('#link-threshold').type('{uparrow}');
-        }
-
-        cy.wait(2000);
-        cy.window().then((win: any) => {
-          expect(win.commonService.session.style.widgets['link-threshold']).to.eq(22);
-          expect(win.commonService.session.data.clusters.length).to.eq(expectedClusterCount)
-        });
+        setGlobalLinkThreshold(22);
+        cy.window()
+          .its('commonService.session.data.clusters')
+          .should('have.length', expectedClusterCount);
 
         cy.get('#epiCurveSVG .epiCurve-epi-curve circle')
-          .its('length')
-          .then((count) => {
-            expect(count).to.be.eq(expectedClusterCount);
-          });
+          .should('have.length', expectedClusterCount);
 
         cy.get('#epiCurveSVG .epiCurve-epi-curve rect')
-          .then(($rects) => {
+          .should(($rects) => {
             const rectFills = [...$rects]
               .map((c) => c.getAttribute('fill') || '')
               .filter(Boolean)
@@ -155,25 +147,17 @@ describe('Epi Curve / Timeline View', () => {
             expect(rectFills.some((fill) => fill === '#b732cc' || fill === 'rgb(183,50,204)' || fill === 'rgb(183, 50, 204)')).to.equal(false);
           });
         
-        for (let i = 0; i < 8; i++) {
-          cy.get('#link-threshold').type('{downarrow}');
-        }
-
-        cy.wait(2000);
-        cy.window().then((win: any) => {
-          expectedClusterCount = 4
-          expect(win.commonService.session.style.widgets['link-threshold']).to.eq(14);
-          expect(win.commonService.session.data.clusters.length).to.eq(expectedClusterCount)
-        });
+        expectedClusterCount = 4
+        setGlobalLinkThreshold(14);
+        cy.window()
+          .its('commonService.session.data.clusters')
+          .should('have.length', expectedClusterCount);
 
         cy.get('#epiCurveSVG .epiCurve-epi-curve circle')
-          .its('length')
-          .then((count) => {
-            expect(count).to.be.eq(expectedClusterCount);
-          });
+          .should('have.length', expectedClusterCount);
 
         cy.get('#epiCurveSVG .epiCurve-epi-curve rect')
-          .then(($rects) => {
+          .should(($rects) => {
             const rectFills = [...$rects]
               .map((c) => c.getAttribute('fill') || '')
               .filter(Boolean)
@@ -200,28 +184,20 @@ describe('Epi Curve / Timeline View', () => {
         cy.window()
           .its('commonService.GlobalSettingsModel.SelectedNodeColorTableTypesVariable')
           .should('equal', 'Show');
-        cy.get('#key-tables-node-table').should('be.visible');
+        cy.get('#node-color-table:visible').should('be.visible');
 
         cy.contains('#global-settings-modal .nav-link', 'Filtering').click();
         let expectedClusterCount = 4
-        for (let i = 0; i < 2; i++) {
-          cy.get('#link-threshold').type('{downarrow}');
-        }
-
-        cy.wait(2000);
-        cy.window().then((win: any) => {
-          expect(win.commonService.session.style.widgets['link-threshold']).to.eq(14);
-          expect(win.commonService.session.data.clusters.length).to.eq(expectedClusterCount)
-        });
+        setGlobalLinkThreshold(14);
+        cy.window()
+          .its('commonService.session.data.clusters')
+          .should('have.length', expectedClusterCount);
 
         cy.get('#epiCurveSVG .epiCurve-epi-curve circle')
-          .its('length')
-          .then((count) => {
-            expect(count).to.be.eq(expectedClusterCount);
-          });
+          .should('have.length', expectedClusterCount);
 
         cy.get('#epiCurveSVG .epiCurve-epi-curve rect')
-          .then(($rects) => {
+          .should(($rects) => {
             const rectFills = [...$rects]
               .map((c) => c.getAttribute('fill') || '')
               .filter(Boolean)
@@ -231,9 +207,9 @@ describe('Epi Curve / Timeline View', () => {
             expect(rectFills.some((fill) => fill === '#b732cc' || fill === 'rgb(183,50,204)' || fill === 'rgb(183, 50, 204)')).to.equal(true);
           });
 
-        cy.get('#key-tables-node-table td input').first().invoke('val', '#777777').trigger('input').trigger('change');
+        cy.get('#node-color-table:visible td input').first().invoke('val', '#777777').trigger('input').trigger('change');
         cy.get('#epiCurveSVG .epiCurve-epi-curve rect')
-          .then(($rects) => {
+          .should(($rects) => {
             const rectFills = [...$rects]
               .map((c) => c.getAttribute('fill') || '')
               .filter(Boolean)
@@ -249,7 +225,7 @@ describe('Epi Curve / Timeline View', () => {
         cy.get('#node-color').invoke('val', '#ff0000').trigger('input');
 
         cy.get('#epiCurveSVG .epiCurve-epi-curve rect')
-          .then(($rects) => {
+          .should(($rects) => {
             const rectFills = [...$rects]
               .map((c) => c.getAttribute('fill') || '')
               .filter(Boolean)
@@ -378,16 +354,26 @@ describe('Epi Curve / Timeline View', () => {
       cy.contains('.p-dialog-title', 'Epi Curve Settings')
       .parents('.p-dialog')
       .within(() => {
-        cy.contains('label', field)
-          .parents('.form-group.row')
-          .first()
-          .find('p-select')
-          .click();
+          cy.contains('label', field)
+            .parents('.form-group.row')
+            .first()
+            .find('p-select')
+            .as('epiFieldSelect')
+            .click();
       });
 
-      cy.get('.p-select-option')
-        .contains(value)
-        .click();
+      // PrimeNG keeps off-screen options in the active listbox so Cypress can
+      // scroll them into view. Scope to the newest listbox without filtering
+      // the option itself through jQuery's stricter :visible semantics.
+      cy.get('[role="listbox"]')
+        .last()
+        .within(() => {
+          cy.contains('.p-select-option', value).click();
+        });
+
+      cy.get('@epiFieldSelect')
+        .find('[role="combobox"]')
+        .should('not.have.attr', 'aria-expanded', 'true');
 
       const normalize = (s: string) => s.replace(/_/g, '').toLowerCase();
       let widgetLocation: string;
@@ -409,7 +395,7 @@ describe('Epi Curve / Timeline View', () => {
 
       cy.window()
         .its(widgetLocation)
-        .then(widgetValue =>
+        .should(widgetValue =>
           expect(normalize(widgetValue)).to.equal(normalize(value))
         )
 
@@ -421,9 +407,8 @@ describe('Epi Curve / Timeline View', () => {
 
         cy.get('#epiCurveSVG .epiCurve-epi-curve text')
           .eq(textBoxNumber)
-          .invoke('text')
-          .then((textValue) => {
-            expect(normalize(textValue)).to.equal(normalize(value));
+          .should(($text) => {
+            expect(normalize($text.text())).to.equal(normalize(value));
           });
       }
     }
@@ -499,7 +484,7 @@ describe('Epi Curve / Timeline View', () => {
         .should('contain.text', `Date (${binSizeLabel} Bins)`);
 
       cy.get('#epiCurveSVG .epiCurve-epi-curve rect')
-        .then(($rects) => {
+        .should(($rects) => {
           const nextRectCount = $rects.length;
           const nextFirstRectWidth = Number($rects.first().attr('width') || 0);
 
@@ -553,7 +538,7 @@ describe('Epi Curve / Timeline View', () => {
         .its('commonService.session.style.widgets.epiCurve-cumulative')
         .should('equal', cumulative);
 
-      cy.get('#epiCurveSVG .epiCurve-epi-curve rect').then(($rects) => {
+      cy.get('#epiCurveSVG .epiCurve-epi-curve rect').should(($rects) => {
         const nextHeights = [...$rects].map((rect) => Number(rect.getAttribute('height') || 0));
         expect(nextHeights.length, 'rect count after cumulative toggle').to.be.greaterThan(1);
         expect(nextHeights.length, 'rect count should stay stable after cumulative toggle').to.equal(previousHeights.length);
diff --git a/cypress/fixtures/missing-node-coverage-extra-node.csv b/cypress/fixtures/missing-node-coverage-extra-node.csv
new file mode 100644
index 00000000..3cc9364d
--- /dev/null
+++ b/cypress/fixtures/missing-node-coverage-extra-node.csv
@@ -0,0 +1,2 @@
+id,metadata
+C,gamma
diff --git a/cypress/fixtures/missing-node-coverage-links.csv b/cypress/fixtures/missing-node-coverage-links.csv
new file mode 100644
index 00000000..af41c76d
--- /dev/null
+++ b/cypress/fixtures/missing-node-coverage-links.csv
@@ -0,0 +1,3 @@
+source,target
+A,B
+B,D
diff --git a/cypress/fixtures/missing-node-coverage-matched-links.csv b/cypress/fixtures/missing-node-coverage-matched-links.csv
new file mode 100644
index 00000000..39761f70
--- /dev/null
+++ b/cypress/fixtures/missing-node-coverage-matched-links.csv
@@ -0,0 +1,2 @@
+source,target
+A,B
diff --git a/cypress/fixtures/missing-node-coverage-matched-nodes.csv b/cypress/fixtures/missing-node-coverage-matched-nodes.csv
new file mode 100644
index 00000000..27111748
--- /dev/null
+++ b/cypress/fixtures/missing-node-coverage-matched-nodes.csv
@@ -0,0 +1,3 @@
+id,metadata
+A,alpha
+B,beta
diff --git a/cypress/fixtures/missing-node-coverage-nodes.csv b/cypress/fixtures/missing-node-coverage-nodes.csv
new file mode 100644
index 00000000..2c913979
--- /dev/null
+++ b/cypress/fixtures/missing-node-coverage-nodes.csv
@@ -0,0 +1,4 @@
+id,metadata
+A,alpha
+B,beta
+C,gamma
diff --git a/cypress/support/crosstab-helpers.ts b/cypress/support/crosstab-helpers.ts
index de9ceab4..0fec0878 100644
--- a/cypress/support/crosstab-helpers.ts
+++ b/cypress/support/crosstab-helpers.ts
@@ -257,7 +257,16 @@ export const selectCrosstabField = (
       .should('be.visible')
       .click({ force: true });
 
-    cy.contains('li[role="option"]', label, { timeout: 15000 }).click({ force: true });
+    cy.contains('li[role="option"]:visible', label, { timeout: 15000 })
+      .should('be.visible')
+      .click({ force: true });
+
+    // PrimeNG keeps the listbox DOM measurable during its close transition,
+    // so jQuery's :visible is not a reliable completion signal. Wait for the
+    // owning control to report that it is no longer expanded instead.
+    cy.get(dialogAlias)
+      .find(`#${selectId} [role="combobox"]`)
+      .should('not.have.attr', 'aria-expanded', 'true');
 
     cy.window()
       .its(`commonService.session.style.widgets.${expectedWidgetKey}`)
diff --git a/cypress/support/journey-helpers.ts b/cypress/support/journey-helpers.ts
index 3f8454ee..a733da51 100644
--- a/cypress/support/journey-helpers.ts
+++ b/cypress/support/journey-helpers.ts
@@ -681,9 +681,27 @@ export function applyPreLaunchFileSettings(profile: DatasetProfile): void {
   });
 }
 
+export function continuePastMissingNodeCoverageWarning(): void {
+  cy.get('body').then(($body) => {
+    const coverageDialog = $body
+      .find(byTestId(testIds.filesMissingNodeCoverageDialog))
+      .filter(':visible')
+      .closest('.p-dialog');
+
+    if (!coverageDialog.length) {
+      return;
+    }
+
+    cy.wrap(coverageDialog)
+      .find(byTestId(testIds.filesMissingNodeCoverageContinue))
+      .click({ force: true });
+  });
+}
+
 export function launchAndWaitForProcessing(timeout = 60000): void {
   cy.get('#launch', { timeout: 15000 }).should('not.be.disabled');
   cy.get('#launch').click({ force: true });
+  continuePastMissingNodeCoverageWarning();
   cy.get('#loading-information', { timeout }).should('not.exist');
   cy.window({ timeout })
     .its('commonService.session.network.isFullyLoaded')
@@ -785,9 +803,22 @@ export function assertCrosstabReady(timeout = 30000): void {
     .should('exist');
 }
 
+function focusOpenedView(viewName: string, timeout = 15000): void {
+  cy.window({ timeout })
+    .should((win: unknown) => {
+      const app = (win as WinWithMT).commonService?.visuals?.microbeTrace;
+      const openViews = (app?.homepageTabs || []).map((tab: { label: string }) => tab.label);
+      expect(openViews, 'open dashboard views').to.include(viewName);
+    })
+    .then((win: unknown) => {
+      const app = (win as WinWithMT).commonService.visuals.microbeTrace;
+      app.Viewclick(viewName);
+    });
+}
+
 export function assertEpiCurveReady(timeout = 30000): void {
-  cy.get('#epiCurve', { timeout }).should('be.visible');
-  cy.get('#epiCurveSVG', { timeout }).should('be.visible');
+  cy.get('#epiCurve:visible', { timeout }).should('be.visible');
+  cy.get('#epiCurve:visible #epiCurveSVG', { timeout }).should('be.visible');
   cy.window({ timeout })
     .its('commonService.visuals.epiCurve')
     .should('exist');
@@ -802,8 +833,8 @@ export function assertWaterfallReady(timeout = 30000): void {
 }
 
 export function assertHeatmapReady(timeout = 30000): void {
-  cy.get('#heatmap', { timeout }).should('be.visible');
-  cy.get('#heatmap svg.main-svg', { timeout }).should('exist');
+  cy.get('#heatmap:visible', { timeout }).should('be.visible');
+  cy.get('#heatmap:visible svg.main-svg', { timeout }).should('exist');
   cy.window({ timeout })
     .its('commonService.visuals.heatmap')
     .should('exist');
@@ -915,6 +946,7 @@ export function goToEpiCurveView(): void {
   cy.get(byTestId(testIds.appViewMenuButton), { timeout: 15000 }).click({ force: true });
   cy.contains('button[mat-menu-item]', 'Epi Curve', { timeout: 15000 }).click({ force: true });
 
+  focusOpenedView('Epi Curve');
   assertEpiCurveReady();
 }
 
@@ -929,6 +961,7 @@ export function goToHeatmapView(): void {
   cy.get(byTestId(testIds.appViewMenuButton), { timeout: 15000 }).click({ force: true });
   cy.contains('button[mat-menu-item]', 'Heatmap', { timeout: 15000 }).click({ force: true });
 
+  focusOpenedView('Heatmap');
   assertHeatmapReady();
 }
 
diff --git a/cypress/support/selectors.ts b/cypress/support/selectors.ts
index d3c53c0c..c31a1c7f 100644
--- a/cypress/support/selectors.ts
+++ b/cypress/support/selectors.ts
@@ -20,6 +20,12 @@ export const testIds = {
   filesSmartLaunchButton: 'files-smart-launch-button',
   filesSmartLaunchInfo: 'files-smart-launch-info',
   filesSmartLaunchTooltip: 'files-smart-launch-tooltip',
+  filesUpdateButton: 'files-update-button',
+  filesMissingNodeCoverageDialog: 'files-missing-node-coverage-dialog',
+  filesMissingNodeCoverageCancel: 'files-missing-node-coverage-cancel',
+  filesMissingNodeCoverageContinue: 'files-missing-node-coverage-continue',
+  filesMissingNodeDataSection: 'files-missing-node-data-section',
+  filesMissingLinkInformationSection: 'files-missing-link-information-section',
   filterEpsilon: 'filter-epsilon',
   filterMinimumClusterSize: 'filter-minimum-cluster-size',
   filterRevealEverything: 'filter-reveal-everything',
diff --git a/examples/issue-1728-node-coverage/01-mismatch-links.csv b/examples/issue-1728-node-coverage/01-mismatch-links.csv
new file mode 100644
index 00000000..3f3fcb3f
--- /dev/null
+++ b/examples/issue-1728-node-coverage/01-mismatch-links.csv
@@ -0,0 +1,3 @@
+source,target,relationship
+A,B,contact
+B,D,contact
diff --git a/examples/issue-1728-node-coverage/01-mismatch-nodes.csv b/examples/issue-1728-node-coverage/01-mismatch-nodes.csv
new file mode 100644
index 00000000..2c913979
--- /dev/null
+++ b/examples/issue-1728-node-coverage/01-mismatch-nodes.csv
@@ -0,0 +1,4 @@
+id,metadata
+A,alpha
+B,beta
+C,gamma
diff --git a/examples/issue-1728-node-coverage/02-matched-links.csv b/examples/issue-1728-node-coverage/02-matched-links.csv
new file mode 100644
index 00000000..a3c0316f
--- /dev/null
+++ b/examples/issue-1728-node-coverage/02-matched-links.csv
@@ -0,0 +1,2 @@
+source,target,relationship
+A,B,contact
diff --git a/examples/issue-1728-node-coverage/02-matched-nodes.csv b/examples/issue-1728-node-coverage/02-matched-nodes.csv
new file mode 100644
index 00000000..27111748
--- /dev/null
+++ b/examples/issue-1728-node-coverage/02-matched-nodes.csv
@@ -0,0 +1,3 @@
+id,metadata
+A,alpha
+B,beta
diff --git a/examples/issue-1728-node-coverage/03-topology-only-links.csv b/examples/issue-1728-node-coverage/03-topology-only-links.csv
new file mode 100644
index 00000000..e1ddc8db
--- /dev/null
+++ b/examples/issue-1728-node-coverage/03-topology-only-links.csv
@@ -0,0 +1,3 @@
+source,target,relationship
+A,B,contact
+B,C,contact
diff --git a/examples/issue-1728-node-coverage/04-node-only-nodes.csv b/examples/issue-1728-node-coverage/04-node-only-nodes.csv
new file mode 100644
index 00000000..2c913979
--- /dev/null
+++ b/examples/issue-1728-node-coverage/04-node-only-nodes.csv
@@ -0,0 +1,4 @@
+id,metadata
+A,alpha
+B,beta
+C,gamma
diff --git a/examples/issue-1728-node-coverage/05-standalone-sequences.fasta b/examples/issue-1728-node-coverage/05-standalone-sequences.fasta
new file mode 100644
index 00000000..d091c28c
--- /dev/null
+++ b/examples/issue-1728-node-coverage/05-standalone-sequences.fasta
@@ -0,0 +1,6 @@
+>A
+ACGTACGT
+>B
+ACGTACGA
+>C
+ACGTTCGA
diff --git a/examples/issue-1728-node-coverage/06-remapped-links.csv b/examples/issue-1728-node-coverage/06-remapped-links.csv
new file mode 100644
index 00000000..ae4c8a9c
--- /dev/null
+++ b/examples/issue-1728-node-coverage/06-remapped-links.csv
@@ -0,0 +1,3 @@
+from_id,to_id,relationship
+X,Y,contact
+Y,W,contact
diff --git a/examples/issue-1728-node-coverage/06-remapped-nodes.csv b/examples/issue-1728-node-coverage/06-remapped-nodes.csv
new file mode 100644
index 00000000..03f255c1
--- /dev/null
+++ b/examples/issue-1728-node-coverage/06-remapped-nodes.csv
@@ -0,0 +1,4 @@
+sample_code,group
+X,one
+Y,one
+Z,two
diff --git a/examples/issue-1728-node-coverage/07-undeclared-endpoint.graphml b/examples/issue-1728-node-coverage/07-undeclared-endpoint.graphml
new file mode 100644
index 00000000..64e8f028
--- /dev/null
+++ b/examples/issue-1728-node-coverage/07-undeclared-endpoint.graphml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<graphml xmlns="http://graphml.graphdrawing.org/xmlns">
+  <graph id="G" edgedefault="undirected">
+    <node id="A" />
+    <node id="B" />
+    <edge id="e1" source="B" target="C" />
+  </graph>
+</graphml>
diff --git a/examples/issue-1728-node-coverage/08-matched-tree.newick b/examples/issue-1728-node-coverage/08-matched-tree.newick
new file mode 100644
index 00000000..db7ea1ac
--- /dev/null
+++ b/examples/issue-1728-node-coverage/08-matched-tree.newick
@@ -0,0 +1 @@
+(A:0.1,(B:0.2,C:0.3):0.1);
diff --git a/examples/issue-1728-node-coverage/09-unmatched-enrichment.geojson b/examples/issue-1728-node-coverage/09-unmatched-enrichment.geojson
new file mode 100644
index 00000000..4454fcf7
--- /dev/null
+++ b/examples/issue-1728-node-coverage/09-unmatched-enrichment.geojson
@@ -0,0 +1,16 @@
+{
+  "type": "FeatureCollection",
+  "features": [
+    {
+      "type": "Feature",
+      "geometry": {
+        "type": "Point",
+        "coordinates": [-84.39, 33.75]
+      },
+      "properties": {
+        "id": "Z",
+        "label": "Enrichment-only identifier"
+      }
+    }
+  ]
+}
diff --git a/examples/issue-1728-node-coverage/10-self-links-links.csv b/examples/issue-1728-node-coverage/10-self-links-links.csv
new file mode 100644
index 00000000..7c752b68
--- /dev/null
+++ b/examples/issue-1728-node-coverage/10-self-links-links.csv
@@ -0,0 +1,5 @@
+source,target,relationship
+A,A,self
+A,B,contact
+B,B,self
+C,C,self
diff --git a/examples/issue-1728-node-coverage/10-self-links-nodes.csv b/examples/issue-1728-node-coverage/10-self-links-nodes.csv
new file mode 100644
index 00000000..2c913979
--- /dev/null
+++ b/examples/issue-1728-node-coverage/10-self-links-nodes.csv
@@ -0,0 +1,4 @@
+id,metadata
+A,alpha
+B,beta
+C,gamma
diff --git a/examples/issue-1728-node-coverage/11-case-sensitive-links.csv b/examples/issue-1728-node-coverage/11-case-sensitive-links.csv
new file mode 100644
index 00000000..a3c0316f
--- /dev/null
+++ b/examples/issue-1728-node-coverage/11-case-sensitive-links.csv
@@ -0,0 +1,2 @@
+source,target,relationship
+A,B,contact
diff --git a/examples/issue-1728-node-coverage/11-case-sensitive-nodes.csv b/examples/issue-1728-node-coverage/11-case-sensitive-nodes.csv
new file mode 100644
index 00000000..086ecd76
--- /dev/null
+++ b/examples/issue-1728-node-coverage/11-case-sensitive-nodes.csv
@@ -0,0 +1,3 @@
+id,metadata
+a,lowercase
+B,uppercase
diff --git a/examples/issue-1728-node-coverage/README.md b/examples/issue-1728-node-coverage/README.md
new file mode 100644
index 00000000..78240ed7
--- /dev/null
+++ b/examples/issue-1728-node-coverage/README.md
@@ -0,0 +1,128 @@
+# Issue 1728: Node Coverage Test Data
+
+Upload the files for one scenario at a time from the Files view. For CSV files,
+confirm the listed file type and field mappings before launching.
+
+## 1. Mismatch in both directions
+
+Files:
+
+- `01-mismatch-nodes.csv` as Node List, ID = `id`
+- `01-mismatch-links.csv` as Link List, Source = `source`, Target = `target`
+
+Expected warning:
+
+- Missing node data (1): `D`
+- Missing link information (1): `C`
+
+Cancel should leave both files loaded and the current network unchanged. Continue
+should launch a network containing the identifiers represented by ingestion.
+
+## 2. Fully matched node and link files
+
+Files:
+
+- `02-matched-nodes.csv` as Node List, ID = `id`
+- `02-matched-links.csv` as Link List, Source = `source`, Target = `target`
+
+Expected: no coverage warning.
+
+## 3. Topology-only link file
+
+File:
+
+- `03-topology-only-links.csv` as Link List, Source = `source`, Target = `target`
+
+Expected warning:
+
+- Missing node data (3): `A`, `B`, `C`
+- No missing-link-information section
+
+## 4. Node-only file
+
+File:
+
+- `04-node-only-nodes.csv` as Node List, ID = `id`
+
+Expected: no coverage warning because there is no explicit topology source.
+
+## 5. Standalone FASTA
+
+File:
+
+- `05-standalone-sequences.fasta` as FASTA
+
+Expected: no coverage warning because sequence-derived links do not exist yet.
+
+## 6. Custom field mappings
+
+Files:
+
+- `06-remapped-nodes.csv` as Node List, ID = `sample_code`
+- `06-remapped-links.csv` as Link List, Source = `from_id`, Target = `to_id`
+
+Expected warning:
+
+- Missing node data (1): `W`
+- Missing link information (1): `Z`
+
+## 7. GraphML with an undeclared edge endpoint
+
+File:
+
+- `07-undeclared-endpoint.graphml` as GraphML
+
+Expected warning:
+
+- Missing node data (1): `C`
+- Missing link information (1): `A`
+
+This verifies that declared GraphML nodes and edge endpoints are analyzed
+separately.
+
+## 8. Newick tree
+
+File:
+
+- `08-matched-tree.newick` as Newick
+
+Expected: no coverage warning. Newick leaves count as both node and topology IDs.
+
+## 9. GeoJSON remains enrichment-only
+
+Files:
+
+- `02-matched-nodes.csv` as Node List, ID = `id`
+- `02-matched-links.csv` as Link List, Source = `source`, Target = `target`
+- `09-unmatched-enrichment.geojson` as GeoJSON
+
+Expected: no coverage warning. The unmatched identifier `Z` in the GeoJSON file
+does not participate in coverage analysis.
+
+## 10. Self-links are ignored
+
+Files:
+
+- `10-self-links-nodes.csv` as Node List, ID = `id`
+- `10-self-links-links.csv` as Link List, Source = `source`, Target = `target`
+
+Expected warning:
+
+- No missing-node-data section
+- Missing link information (1): `C`
+
+The `A-A`, `B-B`, and `C-C` rows are ignored. Only the valid `A-B` topology
+contributes endpoint IDs.
+
+## 11. IDs remain case-sensitive
+
+Files:
+
+- `11-case-sensitive-nodes.csv` as Node List, ID = `id`
+- `11-case-sensitive-links.csv` as Link List, Source = `source`, Target = `target`
+
+Expected warning:
+
+- Missing node data (1): `A`
+- Missing link information (1): `a`
+
diff --git a/src/app/contactTraceCommonServices/import-node-coverage.service.spec.ts b/src/app/contactTraceCommonServices/import-node-coverage.service.spec.ts
new file mode 100644
index 00000000..3263927e
--- /dev/null
+++ b/src/app/contactTraceCommonServices/import-node-coverage.service.spec.ts
@@ -0,0 +1,314 @@
+import * as XLSX from 'xlsx';
+import { GraphMLService } from './graphml.service';
+import {
+  IMPORT_NODE_COVERAGE_DISPLAY_LIMIT,
+  ImportNodeCoverageService,
+} from './import-node-coverage.service';
+
+describe('ImportNodeCoverageService', () => {
+  let service: ImportNodeCoverageService;
+
+  beforeEach(() => {
+    service = new ImportNodeCoverageService(new GraphMLService());
+  });
+
+  it('finds normalized, deduplicated mismatches in both directions', () => {
+    const result = service.analyze([
+      {
+        name: 'nodes.csv',
+        extension: 'csv',
+        format: 'node',
+        field1: 'sample',
+        contents: 'sample,value\n A ,one\nB,two\nB,duplicate\nC,three\n,blank',
+      },
+      {
+        name: 'links.csv',
+        extension: 'csv',
+        format: 'link',
+        field1: 'from',
+        field2: 'to',
+        contents: 'from,to\nA,B\nB,D\nD,D\n,ignored',
+      },
+    ]);
+
+    expect(result.status).toBe('complete');
+    if (result.status !== 'complete') return;
+
+    expect(result.summary.missingNodeData).toEqual({
+      total: 1,
+      ids: ['D'],
+      hidden: 0,
+    });
+    expect(result.summary.missingLinkInformation).toEqual({
+      total: 1,
+      ids: ['C'],
+      hidden: 0,
+    });
+  });
+
+  it('honors remapped JSON fields and preserves case', () => {
+    const result = service.analyze([
+      {
+        name: 'nodes.json',
+        extension: 'json',
+        format: 'node',
+        field1: 'chosenId',
+        contents: JSON.stringify([
+          { ignored: 'wrong-1', chosenId: 'CaseA' },
+          { ignored: 'wrong-2', chosenId: 'casea' },
+        ]),
+      },
+      {
+        name: 'links.json',
+        extension: 'json',
+        format: 'link',
+        field1: 'left',
+        field2: 'right',
+        contents: JSON.stringify([{ left: 'CaseA', right: 'Other' }]),
+      },
+    ]);
+
+    expect(result.status).toBe('complete');
+    if (result.status !== 'complete') return;
+
+    expect(result.summary.missingNodeData.ids).toEqual(['Other']);
+    expect(result.summary.missingLinkInformation.ids).toEqual(['casea']);
+  });
+
+  it('caps each displayed mismatch group at 100 sorted IDs', () => {
+    const nodeRows = Array.from(
+      { length: IMPORT_NODE_COVERAGE_DISPLAY_LIMIT + 5 },
+      (_, index) => `N${index + 1}`,
+    );
+    const result = service.analyze([
+      {
+        name: 'nodes.csv',
+        extension: 'csv',
+        format: 'node',
+        field1: 'id',
+        contents: `id\n${nodeRows.join('\n')}`,
+      },
+      {
+        name: 'links.csv',
+        extension: 'csv',
+        format: 'link',
+        field1: 'source',
+        field2: 'target',
+        contents: 'source,target\nA,B',
+      },
+    ]);
+
+    expect(result.status).toBe('complete');
+    if (result.status !== 'complete') return;
+
+    expect(result.summary.missingLinkInformation.total).toBe(105);
+    expect(result.summary.missingLinkInformation.ids.length).toBe(100);
+    expect(result.summary.missingLinkInformation.hidden).toBe(5);
+    expect(result.summary.missingLinkInformation.ids.slice(0, 3)).toEqual(['N1', 'N2', 'N3']);
+  });
+
+  it('skips node and FASTA inputs when no explicit topology exists', () => {
+    const result = service.analyze([
+      {
+        name: 'nodes.csv',
+        extension: 'csv',
+        format: 'node',
+        field1: 'id',
+        contents: 'id\nA\nB',
+      },
+      {
+        name: 'sequences.fasta',
+        extension: 'fasta',
+        format: 'fasta',
+        contents: '>A\nAAAA\n>B\nCCCC',
+      },
+      {
+        name: 'locations.geojson',
+        extension: 'geojson',
+        format: 'geojson',
+        contents: '{"type":"FeatureCollection","features":[]}',
+      },
+    ]);
+
+    expect(result).toEqual({ status: 'skipped' });
+  });
+
+  it('treats matrices, Newick, and Auspice leaves as node and topology coverage', () => {
+    const result = service.analyze([
+      {
+        name: 'matrix.csv',
+        extension: 'csv',
+        format: 'matrix',
+        contents: ',M1,M2\nM1,0,1\nM2,1,0',
+      },
+      {
+        name: 'tree.nwk',
+        extension: 'nwk',
+        format: 'newick',
+        contents: '(N1:1,N2:1);',
+      },
+      {
+        name: 'auspice.json',
+        extension: 'json',
+        format: 'auspice',
+        contents: {
+          tree: {
+            name: 'root',
+            children: [{ name: 'A1' }, { name: 'A2' }],
+          },
+        },
+      },
+    ]);
+
+    expect(result.status).toBe('complete');
+    if (result.status !== 'complete') return;
+
+    expect(result.summary.missingNodeData.total).toBe(0);
+    expect(result.summary.missingLinkInformation.total).toBe(0);
+  });
+
+  it('reads remapped Excel node and link identifiers', () => {
+    const makeWorkbook = (rows: Record<string, any>[]) => {
+      const workbook = XLSX.utils.book_new();
+      XLSX.utils.book_append_sheet(workbook, XLSX.utils.json_to_sheet(rows), 'Sheet1');
+      return XLSX.write(workbook, { type: 'array', bookType: 'xlsx' });
+    };
+    const result = service.analyze([
+      {
+        name: 'nodes.xlsx',
+        extension: 'xlsx',
+        format: 'node',
+        field1: 'chosen',
+        contents: makeWorkbook([{ other: 'wrong', chosen: 'X1' }]),
+      },
+      {
+        name: 'links.xlsx',
+        extension: 'xlsx',
+        format: 'link',
+        field1: 'left',
+        field2: 'right',
+        contents: makeWorkbook([{ left: 'X1', right: 'X2' }]),
+      },
+    ]);
+
+    expect(result.status).toBe('complete');
+    if (result.status !== 'complete') return;
+
+    expect(result.summary.missingNodeData.ids).toEqual(['X2']);
+    expect(result.summary.missingLinkInformation.total).toBe(0);
+  });
+
+  it('compares declared nodes and endpoints in supported network documents', () => {
+    const result = service.analyze([
+      {
+        name: 'network.dot',
+        extension: 'dot',
+        format: 'network',
+        contents: 'graph G { A; B; C; A -- B; }',
+      },
+    ]);
+
+    expect(result.status).toBe('complete');
+    if (result.status !== 'complete') return;
+
+    expect(result.summary.missingNodeData.total).toBe(0);
+    expect(result.summary.missingLinkInformation.ids).toEqual(['C']);
+  });
+
+  it('does not count generated network endpoint nodes as declarations', () => {
+    const result = service.analyze([
+      {
+        name: 'network.graphml',
+        extension: 'graphml',
+        format: 'network',
+        contents: [
+          '<graphml xmlns="http://graphml.graphdrawing.org/xmlns">',
+          '<graph id="G" edgedefault="undirected">',
+          '<node id="declared"/>',
+          '<edge source="declared" target="endpoint-only"/>',
+          '</graph>',
+          '</graphml>',
+        ].join(''),
+      },
+    ]);
+
+    expect(result.status).toBe('complete');
+    if (result.status !== 'complete') return;
+
+    expect(result.summary.missingNodeData.ids).toEqual(['endpoint-only']);
+    expect(result.summary.missingLinkInformation.total).toBe(0);
+  });
+
+  it('analyzes each supported network document family through the shared importer', () => {
+    const documents = [
+      {
+        name: 'network.graphml',
+        contents: '<graphml xmlns="http://graphml.graphdrawing.org/xmlns"><graph id="G" edgedefault="undirected"><node id="1"/><node id="2"/><node id="3"/><edge source="1" target="2"/></graph></graphml>',
+      },
+      {
+        name: 'network.gexf',
+        contents: '<gexf xmlns="http://gexf.net/1.3"><graph defaultedgetype="undirected"><nodes><node id="1"/><node id="2"/><node id="3"/></nodes><edges><edge id="e1" source="1" target="2"/></edges></graph></gexf>',
+      },
+      {
+        name: 'network.xgmml',
+        contents: '<graph id="G" directed="0" xmlns="http://www.cs.rpi.edu/XGMML"><node id="1"/><node id="2"/><node id="3"/><edge source="1" target="2"/></graph>',
+      },
+      {
+        name: 'network.cx2',
+        contents: JSON.stringify([
+          { CXVersion: '2.0' },
+          { nodes: [{ id: 1 }, { id: 2 }, { id: 3 }] },
+          { edges: [{ id: 1, s: 1, t: 2 }] },
+          { status: [{ success: true }] },
+        ]),
+      },
+      {
+        name: 'network.dot',
+        contents: 'graph G { 1; 2; 3; 1 -- 2; }',
+      },
+      {
+        name: 'network.gv',
+        contents: 'graph G { 1; 2; 3; 1 -- 2; }',
+      },
+      {
+        name: 'network.gml',
+        contents: 'graph [ node [ id 1 ] node [ id 2 ] node [ id 3 ] edge [ source 1 target 2 ] ]',
+      },
+    ];
+
+    documents.forEach(document => {
+      const result = service.analyze([{
+        ...document,
+        extension: document.name.split('.').pop(),
+        format: 'network',
+      }]);
+
+      expect(result.status).withContext(document.name).toBe('complete');
+      if (result.status !== 'complete') return;
+      expect(result.summary.missingNodeData.total).withContext(document.name).toBe(0);
+      expect(result.summary.missingLinkInformation.ids).withContext(document.name).toEqual(['3']);
+    });
+  });
+
+  it('returns unavailable instead of a partial result when a contributing file cannot be parsed', () => {
+    const result = service.analyze([
+      {
+        name: 'nodes.csv',
+        extension: 'csv',
+        format: 'node',
+        field1: 'id',
+        contents: 'id\nA',
+      },
+      {
+        name: 'broken.json',
+        extension: 'json',
+        format: 'link',
+        field1: 'source',
+        field2: 'target',
+        contents: '{not json}',
+      },
+    ]);
+
+    expect(result.status).toBe('unavailable');
+  });
+});
diff --git a/src/app/contactTraceCommonServices/import-node-coverage.service.ts b/src/app/contactTraceCommonServices/import-node-coverage.service.ts
new file mode 100644
index 00000000..a0f6d8ca
--- /dev/null
+++ b/src/app/contactTraceCommonServices/import-node-coverage.service.ts
@@ -0,0 +1,309 @@
+import { Injectable } from '@angular/core';
+import * as Papa from 'papaparse';
+import * as patristic from 'patristic';
+import * as XLSX from 'xlsx';
+import { GraphMLService } from './graphml.service';
+
+export const IMPORT_NODE_COVERAGE_DISPLAY_LIMIT = 100;
+
+export interface ImportNodeCoverageGroup {
+  total: number;
+  ids: string[];
+  hidden: number;
+}
+
+export interface ImportNodeCoverageSummary {
+  missingNodeData: ImportNodeCoverageGroup;
+  missingLinkInformation: ImportNodeCoverageGroup;
+}
+
+export type ImportNodeCoverageAnalysis =
+  | { status: 'complete'; summary: ImportNodeCoverageSummary }
+  | { status: 'skipped' }
+  | { status: 'unavailable'; error: unknown };
+
+interface ImportCoverageAccumulator {
+  nodeIds: Set<string>;
+  topologyIds: Set<string>;
+  hasExplicitTopology: boolean;
+}
+
+@Injectable({
+  providedIn: 'root'
+})
+export class ImportNodeCoverageService {
+  constructor(private graphMLService: GraphMLService) {}
+
+  analyze(files: ReadonlyArray<any>): ImportNodeCoverageAnalysis {
+    const coverage: ImportCoverageAccumulator = {
+      nodeIds: new Set<string>(),
+      topologyIds: new Set<string>(),
+      hasExplicitTopology: false,
+    };
+
+    try {
+      for (const file of files || []) {
+        this.addFileCoverage(file, coverage);
+      }
+    } catch (error) {
+      console.warn('Unable to complete the missing-node import preflight.', error);
+      return { status: 'unavailable', error };
+    }
+
+    if (!coverage.hasExplicitTopology) {
+      return { status: 'skipped' };
+    }
+
+    const missingNodeData = Array.from(coverage.topologyIds)
+      .filter(id => !coverage.nodeIds.has(id));
+    const missingLinkInformation = Array.from(coverage.nodeIds)
+      .filter(id => !coverage.topologyIds.has(id));
+
+    return {
+      status: 'complete',
+      summary: {
+        missingNodeData: this.summarize(missingNodeData),
+        missingLinkInformation: this.summarize(missingLinkInformation),
+      }
+    };
+  }
+
+  private addFileCoverage(file: any, coverage: ImportCoverageAccumulator): void {
+    const format = String(file?.format ?? '').toLowerCase();
+
+    switch (format) {
+      case 'node':
+        this.addNodeTableCoverage(file, coverage);
+        return;
+      case 'link':
+        this.addLinkTableCoverage(file, coverage);
+        return;
+      case 'matrix':
+        this.addMatrixCoverage(file, coverage);
+        return;
+      case 'fasta':
+        this.addFastaCoverage(file, coverage);
+        return;
+      case 'newick':
+        this.addNewickCoverage(file, coverage);
+        return;
+      case 'auspice':
+        this.addAuspiceCoverage(file, coverage);
+        return;
+      case 'network':
+      case 'graphml':
+        this.addNetworkDocumentCoverage(file, coverage);
+        return;
+      // GeoJSON enriches nodes that another source creates. Session/style and
+      // unknown files likewise do not define either side of this comparison.
+      case 'geojson':
+      default:
+        return;
+    }
+  }
+
+  private addNodeTableCoverage(file: any, coverage: ImportCoverageAccumulator): void {
+    const idField = String(file?.field1 ?? '');
+    this.readTableRecords(file).forEach(record => {
+      this.addId(coverage.nodeIds, record?.[idField]);
+    });
+  }
+
+  private addLinkTableCoverage(file: any, coverage: ImportCoverageAccumulator): void {
+    coverage.hasExplicitTopology = true;
+    const sourceField = String(file?.field1 ?? '');
+    const targetField = String(file?.field2 ?? '');
+
+    this.readTableRecords(file).forEach(record => {
+      this.addTopologyPair(
+        coverage.topologyIds,
+        record?.[sourceField],
+        record?.[targetField],
+      );
+    });
+  }
+
+  private addMatrixCoverage(file: any, coverage: ImportCoverageAccumulator): void {
+    coverage.hasExplicitTopology = true;
+    const rows = this.readMatrixRows(file);
+    if (!rows.length) {
+      return;
+    }
+
+    const ids = new Set<string>();
+    rows[0].slice(1).forEach(value => this.addId(ids, value));
+    rows.slice(1).forEach(row => this.addId(ids, row?.[0]));
+    ids.forEach(id => {
+      coverage.nodeIds.add(id);
+      coverage.topologyIds.add(id);
+    });
+  }
+
+  private addFastaCoverage(file: any, coverage: ImportCoverageAccumulator): void {
+    const contents = String(file?.contents ?? '');
+    contents.split(/[\r\n]+/g).forEach(line => {
+      if (line.startsWith('>')) {
+        this.addId(coverage.nodeIds, line.slice(1));
+      }
+    });
+  }
+
+  private addNewickCoverage(file: any, coverage: ImportCoverageAccumulator): void {
+    coverage.hasExplicitTopology = true;
+    const tree = patristic.parseNewick(String(file?.contents ?? ''));
+    tree.getLeaves().forEach(leaf => {
+      const id = this.normalizeId(leaf?.id);
+      if (!id) {
+        return;
+      }
+
+      coverage.nodeIds.add(id);
+      coverage.topologyIds.add(id);
+    });
+  }
+
+  private addAuspiceCoverage(file: any, coverage: ImportCoverageAccumulator): void {
+    coverage.hasExplicitTopology = true;
+    const contents = typeof file?.contents === 'string'
+      ? JSON.parse(file.contents)
+      : file?.contents;
+    const root = contents?.tree;
+    if (!root || typeof root !== 'object') {
+      throw new Error(`Auspice file ${file?.name || ''} does not contain a tree.`);
+    }
+
+    const visit = (node: any): void => {
+      const children = Array.isArray(node?.children) ? node.children : [];
+      if (!children.length) {
+        const id = this.normalizeId(node?.name);
+        if (id) {
+          coverage.nodeIds.add(id);
+          coverage.topologyIds.add(id);
+        }
+        return;
+      }
+
+      children.forEach(visit);
+    };
+
+    visit(root);
+  }
+
+  private addNetworkDocumentCoverage(file: any, coverage: ImportCoverageAccumulator): void {
+    coverage.hasExplicitTopology = true;
+    const document = this.graphMLService.importNetworkDocument(file?.contents, {
+      sourceName: file?.name,
+    });
+
+    document.nodes
+      .filter(node => node?.mt_generated_endpoint !== true && node?.dot_implicit_node !== true)
+      .forEach(node => this.addId(coverage.nodeIds, node?._id ?? node?.id));
+    document.links.forEach(link => {
+      this.addTopologyPair(coverage.topologyIds, link?.source, link?.target);
+    });
+  }
+
+  private readTableRecords(file: any): any[] {
+    const extension = this.getExtension(file);
+    if (extension === 'xls' || extension === 'xlsx') {
+      const workbook = XLSX.read(file?.contents, {
+        type: 'array',
+        cellDates: true,
+        dateNF: 'mm/dd/yyyy',
+      });
+      return XLSX.utils.sheet_to_json(
+        workbook.Sheets[workbook.SheetNames[0]],
+        { raw: false, dateNF: 'mm/dd/yyyy' },
+      );
+    }
+
+    if (extension === 'json') {
+      const parsed = typeof file?.contents === 'string'
+        ? JSON.parse(file.contents)
+        : file?.contents;
+      if (Array.isArray(parsed)) {
+        return parsed;
+      }
+      return parsed && typeof parsed === 'object' ? [parsed] : [];
+    }
+
+    const result = Papa.parse<Record<string, any>>(String(file?.contents ?? ''), {
+      header: true,
+      dynamicTyping: true,
+      skipEmptyLines: true,
+    });
+    return result.data;
+  }
+
+  private readMatrixRows(file: any): any[][] {
+    const extension = this.getExtension(file);
+    if (extension === 'xls' || extension === 'xlsx') {
+      const workbook = XLSX.read(file?.contents, {
+        type: 'array',
+        cellDates: true,
+        dateNF: 'mm/dd/yyyy',
+      });
+      return XLSX.utils.sheet_to_json(
+        workbook.Sheets[workbook.SheetNames[0]],
+        { header: 1, raw: true, dateNF: 'mm/dd/yyyy' },
+      ) as any[][];
+    }
+
+    const result = Papa.parse<any[]>(String(file?.contents ?? ''), {
+      skipEmptyLines: 'greedy',
+    });
+    return result.data;
+  }
+
+  private getExtension(file: any): string {
+    const explicit = String(file?.extension ?? '').toLowerCase();
+    if (explicit) {
+      return explicit;
+    }
+
+    const name = String(file?.name ?? '');
+    return name.includes('.') ? name.split('.').pop()?.toLowerCase() || '' : '';
+  }
+
+  private addTopologyPair(ids: Set<string>, rawSource: any, rawTarget: any): void {
+    const source = this.normalizeId(rawSource);
+    const target = this.normalizeId(rawTarget);
+    if (!source || !target || source === target) {
+      return;
+    }
+
+    ids.add(source);
+    ids.add(target);
+  }
+
+  private addId(ids: Set<string>, rawValue: any): void {
+    const id = this.normalizeId(rawValue);
+    if (id) {
+      ids.add(id);
+    }
+  }
+
+  private normalizeId(value: any): string | null {
+    if (value === null || value === undefined) {
+      return null;
+    }
+
+    const id = String(value).trim();
+    return id.length ? id : null;
+  }
+
+  private summarize(ids: string[]): ImportNodeCoverageGroup {
+    const sorted = [...ids].sort((left, right) => left.localeCompare(
+      right,
+      'en',
+      { numeric: true, sensitivity: 'variant' },
+    ));
+    const displayed = sorted.slice(0, IMPORT_NODE_COVERAGE_DISPLAY_LIMIT);
+
+    return {
+      total: sorted.length,
+      ids: displayed,
+      hidden: sorted.length - displayed.length,
+    };
+  }
+}
diff --git a/src/app/filesComponent/files-plugin.component.html b/src/app/filesComponent/files-plugin.component.html
index dc61af2c..ea4b8dcf 100644
--- a/src/app/filesComponent/files-plugin.component.html
+++ b/src/app/filesComponent/files-plugin.component.html
@@ -314,6 +314,79 @@ <h1><b>Please add data files to load...</b></h1>
       </div>
     </p-dialog>
 
+    <p-dialog
+      header="Potentially Missing Node Data"
+      [(visible)]="displayMissingNodeCoverageDialog"
+      [modal]="true"
+      [dismissableMask]="false"
+      [closeOnEscape]="true"
+      [style]="{ width: '42rem', maxWidth: 'calc(100vw - 2rem)' }"
+      appendTo="body"
+      (onHide)="cancelMissingNodeCoverageLaunch()">
+      @if (missingNodeCoverageSummary) {
+        <div data-testid="files-missing-node-coverage-dialog" class="pr-2" style="max-height: min(60vh, 36rem); overflow-y: auto;">
+          <p>
+            Some identifiers are not represented in both the imported node data and the imported link or topology data.
+            You can continue with the available data or cancel and correct the uploaded files.
+            Please upload a corrected dataset.
+          </p>
+
+          @if (missingNodeCoverageSummary.missingNodeData.total > 0) {
+            <section data-testid="files-missing-node-data-section" class="mt-4">
+              <h3 class="h6 font-weight-bold mb-1">Missing node data ({{ missingNodeCoverageSummary.missingNodeData.total }})</h3>
+              <p class="mb-2">These identifiers occur in link or topology data but not in node data.</p>
+              <ol data-testid="files-missing-node-data-list" class="mb-2 pl-4 text-break">
+                @for (nodeId of missingNodeCoverageSummary.missingNodeData.ids; track nodeId) {
+                  <li>{{ nodeId }}</li>
+                }
+              </ol>
+              @if (missingNodeCoverageSummary.missingNodeData.hidden > 0) {
+                <p class="font-italic">
+                  {{ missingNodeCoverageSummary.missingNodeData.hidden }} additional IDs not shown.
+                </p>
+              }
+            </section>
+          }
+
+          @if (missingNodeCoverageSummary.missingLinkInformation.total > 0) {
+            <section data-testid="files-missing-link-information-section" class="mt-4">
+              <h3 class="h6 font-weight-bold mb-1">Missing link information ({{ missingNodeCoverageSummary.missingLinkInformation.total }})</h3>
+              <p class="mb-2">These identifiers occur in node data but not in link or topology data.</p>
+              <ol data-testid="files-missing-link-information-list" class="mb-2 pl-4 text-break">
+                @for (nodeId of missingNodeCoverageSummary.missingLinkInformation.ids; track nodeId) {
+                  <li>{{ nodeId }}</li>
+                }
+              </ol>
+              @if (missingNodeCoverageSummary.missingLinkInformation.hidden > 0) {
+                <p class="font-italic">
+                  {{ missingNodeCoverageSummary.missingLinkInformation.hidden }} additional IDs not shown.
+                </p>
+              }
+            </section>
+          }
+        </div>
+      }
+
+      <ng-template #footer>
+        <div class="d-flex justify-content-end">
+          <button
+            type="button"
+            data-testid="files-missing-node-coverage-cancel"
+            class="btn btn-secondary"
+            (click)="cancelMissingNodeCoverageLaunch()">
+            Cancel
+          </button>
+          <button
+            type="button"
+            data-testid="files-missing-node-coverage-continue"
+            class="btn btn-primary ml-2"
+            (click)="continueMissingNodeCoverageLaunch()">
+            Continue
+          </button>
+        </div>
+      </ng-template>
+    </p-dialog>
+
   </div><div id="file-footer">
   <br/>
 
diff --git a/src/app/filesComponent/files-plugin.component.ts b/src/app/filesComponent/files-plugin.component.ts
index 2ac46e7f..0de0f77c 100644
--- a/src/app/filesComponent/files-plugin.component.ts
+++ b/src/app/filesComponent/files-plugin.component.ts
@@ -7,7 +7,6 @@ import * as fileto from 'fileto';
 import { generateCanvas } from '../visualizationComponents/AlignmentViewComponent/generateAlignmentViewCanvas';
 import * as tn93 from 'tn93';
 import * as patristic from 'patristic';
-import * as _ from 'lodash';
 import JSZip from 'jszip';
 import { EventEmitterService } from '@shared/utils/event-emitter.service';
 import { BaseComponentDirective } from '@app/base-component.directive';
@@ -31,6 +30,10 @@ import { WorkerComputeService } from '@app/contactTraceCommonServices/worker-com
 import { GraphMLService } from '@app/contactTraceCommonServices/graphml.service';
 import { clampNegativeBranchLengthsToZero } from '@app/workers/phylogenetic-tree-utils';
 import { findRecommendedThresholdIndex } from '@app/contactTraceCommonServices/threshold-analysis';
+import {
+  ImportNodeCoverageService,
+  ImportNodeCoverageSummary,
+} from '@app/contactTraceCommonServices/import-node-coverage.service';
 import { FEATURE_FLAGS } from '@app/feature-flags';
 
 interface FileTableOption {
@@ -54,6 +57,12 @@ interface AddToTableOptions {
   predictFields?: boolean;
 }
 
+interface LaunchOptions {
+  resetSettings?: boolean;
+  smartThreshold?: boolean;
+  embedHandoff?: boolean;
+}
+
 
 @Component({
     selector: 'FilesComponent',
@@ -134,11 +143,17 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
   displayFileSettings: boolean = false;
   displaySequenceSettings: boolean = false;
   displayloadingInformationModal: boolean = false;
+  displayMissingNodeCoverageDialog: boolean = false;
+  missingNodeCoverageSummary: ImportNodeCoverageSummary | null = null;
   handoffError: string | null = null;
+  private isCheckingImportCoverage: boolean = false;
   private smartLaunchRequested: boolean = false;
+  private pendingCoverageLaunchOptions: LaunchOptions | null = null;
 
   get hasLaunchableFiles(): boolean {
-    return !this.isLoadingFiles && (this.commonService.session?.files?.length ?? 0) > 0;
+    return !this.isLoadingFiles &&
+      !this.isCheckingImportCoverage &&
+      (this.commonService.session?.files?.length ?? 0) > 0;
   }
 
   readonly fileTableFormatOptions: FileTableOption[] = [
@@ -155,12 +170,6 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
   fileTableRows: FileTableRow[] = [];
   private nextFileTableRowId = 0;
 
-  nodeIds: { fileName: string; ids: string[] }[] = [];
-  edgeIds: { fileName: string; ids: { source: string; target: string }[] }[] = [];
-
-  uniqueNodes: string[] = [];
-  uniqueEdgeNodes: string[] = [];
-
   public title: string;
   public id: string;
 
@@ -183,7 +192,8 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
     private embedHandoffService: EmbedHandoffService,
     private ngZone: NgZone,
     private workerComputeService: WorkerComputeService,
-    private graphMLService: GraphMLService
+    private graphMLService: GraphMLService,
+    private importNodeCoverageService: ImportNodeCoverageService,
     ) {
 
     super(elRef.nativeElement);
@@ -579,7 +589,6 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
       this.commonService.session.files.splice(fileIndex, 1);
     }
 
-    this.removeFile(row.fileName);
     this.fileTableRows = this.fileTableRows.filter(existingRow => existingRow !== row);
 
     if (this.commonService.session.files.length === 0) {
@@ -730,9 +739,6 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
           return;
         }
 
-        this.commonService.session.files.forEach(file => {
-          this.removeFile(file.name, false);
-        });
         this.store.setFP_removeFiles(false);
       });
 
@@ -1442,7 +1448,57 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
    * or resets all settings when requested by the Files tab reset update action.
    * Calls creatLaunchSequences to process the data files loaded.
    */
-  launchClick(options: { resetSettings?: boolean; smartThreshold?: boolean; embedHandoff?: boolean } = {}) {
+  async launchClick(options: LaunchOptions = {}): Promise<void> {
+    if (this.isCheckingImportCoverage || this.displayMissingNodeCoverageDialog) {
+      return;
+    }
+
+    this.isCheckingImportCoverage = true;
+    this.refreshTemplateState();
+
+    // Let the disabled launch state render before parsing large local files.
+    await new Promise<void>(resolve => setTimeout(resolve, 0));
+    const analysis = this.importNodeCoverageService.analyze(this.commonService.session.files);
+
+    this.isCheckingImportCoverage = false;
+    this.refreshTemplateState();
+
+    if (analysis.status === 'complete') {
+      const { missingNodeData, missingLinkInformation } = analysis.summary;
+      if (missingNodeData.total > 0 || missingLinkInformation.total > 0) {
+        this.missingNodeCoverageSummary = analysis.summary;
+        this.pendingCoverageLaunchOptions = { ...options };
+        this.displayMissingNodeCoverageDialog = true;
+        this.refreshTemplateState();
+        return;
+      }
+    }
+
+    this.executeLaunch(options);
+  }
+
+  cancelMissingNodeCoverageLaunch(): void {
+    this.pendingCoverageLaunchOptions = null;
+    this.missingNodeCoverageSummary = null;
+    this.displayMissingNodeCoverageDialog = false;
+    this.refreshTemplateState();
+  }
+
+  continueMissingNodeCoverageLaunch(): void {
+    const options = this.pendingCoverageLaunchOptions;
+    if (!options) {
+      this.cancelMissingNodeCoverageLaunch();
+      return;
+    }
+
+    this.pendingCoverageLaunchOptions = null;
+    this.missingNodeCoverageSummary = null;
+    this.displayMissingNodeCoverageDialog = false;
+    this.refreshTemplateState();
+    this.executeLaunch(options);
+  }
+
+  private executeLaunch(options: LaunchOptions = {}): void {
 
     this.smartLaunchRequested = this.smartLaunchEnabled && options.smartThreshold === true;
 
@@ -2426,19 +2482,6 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
       console.log(nodes);
     }
     this.commonService.session.data.nodeFilteredValues = nodes;
-    //Add links for nodes with no edges
-    // TODO: This was here before but not sure why we needed this
-    // this.uniqueNodes.forEach(x => {
-    //   console.log('link same 4: ', x);
-    //   this.commonService.addLink(Object.assign({
-    //     source: '' + x,
-    //     target: '' + x,
-    //     origin: origin,
-    //     visible: true,
-    //     distance: 0,
-    //   }, 'generated'));
-    // });
-
     this.processSequence(loadGeneration)
   }
 
@@ -2819,16 +2862,11 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
   }
 
   /**
-   * Removes all files from commonService.session.files, sets this.nodeIds and this.edgeIds to empty arrays [].
-   * Calls nodeEdgeCheck
+   * Removes all files from the current Files view.
    */
   removeAllFiles() {
     this.fileTableRows = [];
     this.commonService.session.files = [];
-    this.nodeIds = [];
-    this.edgeIds = [];
-
-    this.nodeEdgeCheck();
     this.refreshTemplateState();
   }
 
@@ -2975,27 +3013,12 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
       }
 
       addTableTile(headers, this);
-      this.nodeEdgeCheck();
     } else if (isNetworkDocument) {
       try {
         const networkDocument = this.graphMLService.importNetworkDocument(file.contents, { sourceName: file.name });
         file.format = 'network';
         const detectedFormat = addTableTile(['network_format', '_id', 'source', 'target', 'distance', 'origin'], this);
-        this.nodeIds = this.nodeIds.filter(x => x.fileName !== file.name);
-        this.edgeIds = this.edgeIds.filter(x => x.fileName !== file.name);
-        this.nodeIds.push({
-          fileName: file.name,
-          ids: networkDocument.nodes.map(node => '' + node._id)
-        });
-        this.edgeIds.push({
-          fileName: file.name,
-          ids: networkDocument.links.map(link => ({
-            source: '' + link.source,
-            target: '' + link.target
-          }))
-        });
         networkDocument.warnings.forEach(warning => console.warn(`Network ${file.name}: ${warning}`));
-        this.nodeEdgeCheck();
         if(this.commonService.debugMode) {
           console.log('addToTable Network detected format: ', detectedFormat, networkDocument);
         }
@@ -3013,39 +3036,19 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
           data = [file.contents];
         }
 
-        const detectedFormat = addTableTile(this.normalizeFileTableHeaders(Object.keys(data[0])), this);
-
-        if (detectedFormat === 'node') {
-          this.loadNodes(file.name, data, true);
-        }
-        if (detectedFormat === 'link') {
-          this.loadEdges(file.name, data, true);
-        }
-
-        this.nodeEdgeCheck();
+        addTableTile(this.normalizeFileTableHeaders(Object.keys(data[0])), this);
 
     } else if (isFasta) {
       //let that = this;
       this.commonService.parseFASTA(file.contents).then((output) => {
         addTableTile(["id", "seq"], this);
-
-        this.nodeEdgeCheck();
         })
     } else {
       Papa.parse(file.contents, {
         header: true,
         skipEmptyLines: true,
         complete: output => {
-          const detectedFormat = addTableTile(this.normalizeFileTableHeaders(output.meta.fields), this);
-
-          if (detectedFormat === 'node') {
-            this.loadNodes(file.name, output, false);
-          }
-          if (detectedFormat === 'link') {
-            this.loadEdges(file.name, output, false);
-          }
-
-          this.nodeEdgeCheck();
+          addTableTile(this.normalizeFileTableHeaders(output.meta.fields), this);
 
           if(this.commonService.debugMode) {
             console.log('addToTable parse end: ', file);
@@ -3097,117 +3100,6 @@ export class FilesComponent extends BaseComponentDirective implements OnInit {
 
   }
 
-  /**
-   * Populates this.nodeIds
-   */
-  loadNodes(fileName: any, output: any, isJson: boolean) {
-    if (isJson) {
-      const data: any[] = output;
-      const firstField = Object.keys(data[0])[0];
-      if (this.nodeIds.find(x => x.fileName === fileName)) {
-        const currentNodeId = this.nodeIds.find(x => x.fileName === fileName)
-        currentNodeId.ids = output.map((x: any) => x[firstField])
-      } else {
-        this.nodeIds.push(
-          {
-            fileName: fileName, ids: output.map((x: any) => ('' + x[firstField]))
-          });
-      }
-
-    }
-    else {
-      if (this.nodeIds.find(x => x.fileName === fileName)) {
-        const currentNodeId = this.nodeIds.find(x => x.fileName === fileName)
-        currentNodeId.ids = output.data.map((x: any) => x[output.meta.fields[0]])
-      } else {
-        this.nodeIds.push(
-          {
-            fileName: fileName, ids: output.data.map((x: any) => ('' + x[output.meta.fields[0]]))
-          });
-      }
-    }
-  }
-
-  /**
-   * Populated this.edgeIds
-   */
-  loadEdges(fileName: any, output: any, isJson: boolean) {
-    if (isJson) {
-      const data: any[] = output;
-      const fields = Object.keys(data[0]);
-      if (this.edgeIds.find(x => x.fileName === fileName)) {
-        const currentEdgeId = this.edgeIds.find(x => x.fileName === fileName)
-        currentEdgeId.ids = output.map((x: any) => ({
-          source: '' + x[fields[0]],
-          target: '' + x[fields[1]]
-        }))
-      } else {
-        console.log(`Adding edges ${output}`);
-        this.edgeIds.push({
-          fileName: fileName,
-          ids: output.map((x: any) => ({
-            source: '' + x[fields[0]],
-            target: '' + x[fields[1]]
-          }))
-        })
-
-      }
-
-    }
-    else {
-      if (this.edgeIds.find(x => x.fileName === fileName)) {
-        const currentEdgeId = this.edgeIds.find(x => x.fileName === fileName)
-        currentEdgeId.ids = output.data.map((x: any) => ({
-          source: '' + x[output.meta.fields[0]],
-          target: '' + x[output.meta.fields[1]]
-        }))
-      } else {
-        this.edgeIds.push({
-          fileName: fileName,
-          ids: output.data.map((x: any) => ({
-            source: '' + x[output.meta.fields[0]],
-            target: '' + x[output.meta.fields[1]]
-          }))
-        })
-
-      }
-    }
-
-  }
-
-  /**
-   * Updates this.uniqueEdgeNodes and this.uniqueNodes
-   */
-  nodeEdgeCheck() {
-    // populated with a string[] of unique node ids
-    let allNodesListNodes: string[] = [];
-    this.nodeIds.forEach(x => {
-      x.ids.forEach(y => allNodesListNodes.push(y));
-    });
-    allNodesListNodes = _.uniq(allNodesListNodes);
-
-    // populated with a string[] of unique node ids that have a link/edge
-    let allEdgeListNodes: string[] = [];
-    this.edgeIds.forEach(x => x.ids.forEach(y => {
-      allEdgeListNodes.push(y.source);
-      allEdgeListNodes.push(y.target);
-    }));
-    allEdgeListNodes = _.uniq(allEdgeListNodes);
-
-    this.uniqueEdgeNodes = allEdgeListNodes.filter(x => x && !allNodesListNodes.some(y=>y==x));
-    this.uniqueNodes = allNodesListNodes.filter(x => x && !this.uniqueEdgeNodes.some(y=>y==x));
-  }
-
-  /**
-   * Removes elements of this.nodeIds and this.edgeIds where the fileName == fileName and then calls nodeEdgeCheck to update uniqueEdgeNodes and uniqueNodes
-   * @param fileName 
-   */
-  removeFile(fileName, runNodeEdgeCheck=true) {
-    this.nodeIds = this.nodeIds.filter(x => x.fileName != fileName);
-    this.edgeIds = this.edgeIds.filter(x => x.fileName != fileName);
-    if (runNodeEdgeCheck) this.nodeEdgeCheck();
-  }
-
   /**
    * Async function that reads sequencing data from fasta files or from csv/excel files with sequence data
    * 
diff --git a/src/app/visualizationComponents/BubbleComponent/bubble.component.ts b/src/app/visualizationComponents/BubbleComponent/bubble.component.ts
index 0651513e..b75fadfa 100644
--- a/src/app/visualizationComponents/BubbleComponent/bubble.component.ts
+++ b/src/app/visualizationComponents/BubbleComponent/bubble.component.ts
@@ -61,6 +61,7 @@ export class BubbleComponent extends BaseComponentDirective implements OnInit, M
   @ViewChild('bubbleTooltip') toolTip: ElementRef;
   
   cy: Core;
+  private resizeTimer: ReturnType<typeof setTimeout> | null = null;
   
   visuals: MicrobeTraceNextVisuals;
   widgets: any;
@@ -227,6 +228,11 @@ export class BubbleComponent extends BaseComponentDirective implements OnInit, M
     this.destroy$.complete();
     $(document).off('.bubbleView');
 
+    if (this.resizeTimer !== null) {
+      clearTimeout(this.resizeTimer);
+      this.resizeTimer = null;
+    }
+
     if (this.cy){
         this.cy.removeAllListeners();
         this.cy.destroy();
@@ -1151,8 +1157,19 @@ export class BubbleComponent extends BaseComponentDirective implements OnInit, M
     this.viewHeight = this.container.height - 73;
     this.viewWidth = this.container.width - 42;
     this.cdref.detectChanges()
-    setTimeout(() => {
-      this.cy.fit(this.cy.nodes(), 30);
+
+    if (this.resizeTimer !== null) {
+      clearTimeout(this.resizeTimer);
+    }
+
+    this.resizeTimer = setTimeout(() => {
+      this.resizeTimer = null;
+      const cy = this.cy;
+      if (!cy || cy.destroyed()) {
+        return;
+      }
+
+      cy.fit(cy.nodes(), 30);
       this.onLabelSizeChange()
     }, 200);
   }
diff --git a/src/app/visualizationComponents/TwoDComponent/twoD-plugin.component.ts b/src/app/visualizationComponents/TwoDComponent/twoD-plugin.component.ts
index 0cf3a8d1..6f0a390d 100644
--- a/src/app/visualizationComponents/TwoDComponent/twoD-plugin.component.ts
+++ b/src/app/visualizationComponents/TwoDComponent/twoD-plugin.component.ts
@@ -5983,7 +5983,7 @@ export class TwoDComponent extends BaseComponentDirective implements OnInit, Mic
                     });
                 });
 
-                cy.collection(group.values).move({ parent: parentId });
+                cy.collection().union(group.values).move({ parent: parentId });
             });
 
             this.applyPolygonLabelStyle();