diff --git a/packages/compiler-cli/src/ngtsc/program_driver/src/ts_create_program_driver.ts b/packages/compiler-cli/src/ngtsc/program_driver/src/ts_create_program_driver.ts
index b07ce198984..8d8dabc4267 100644
--- a/packages/compiler-cli/src/ngtsc/program_driver/src/ts_create_program_driver.ts
+++ b/packages/compiler-cli/src/ngtsc/program_driver/src/ts_create_program_driver.ts
@@ -272,5 +272,12 @@ export class TsCreateProgramDriver implements ProgramDriver {
     // TS 5.5 not having the files tagged while producing diagnostics can lead to errors. See:
     // https://github.com/microsoft/TypeScript/pull/58398
     untagAllTsFiles(oldProgram);
+
+    // Re-tag the new program's files. Since TS reuses SourceFile objects between old and new
+    // programs, untagging the old program also untags shared files in the new program.
+    // Without re-tagging, getSemanticDiagnostics() crashes with "Cannot destructure property
+    // 'pos' of 'file.referencedFiles[index]'" because fileProcessingDiagnostics recorded
+    // indices into the tagged (longer) referencedFiles array during program creation.
+    retagAllTsFiles(this.program);
   }
 }
diff --git a/packages/compiler-cli/src/ngtsc/typecheck/test/program_spec.ts b/packages/compiler-cli/src/ngtsc/typecheck/test/program_spec.ts
index 8ab433802b5..400f95c0569 100644
--- a/packages/compiler-cli/src/ngtsc/typecheck/test/program_spec.ts
+++ b/packages/compiler-cli/src/ngtsc/typecheck/test/program_spec.ts
@@ -11,7 +11,7 @@ import ts from 'typescript';
 import {absoluteFrom, AbsoluteFsPath, getSourceFileOrError} from '../../file_system';
 import {runInEachFileSystem} from '../../file_system/testing';
 import {FileUpdate, TsCreateProgramDriver, UpdateMode} from '../../program_driver';
-import {sfExtensionData, ShimReferenceTagger} from '../../shims';
+import {sfExtensionData, ShimReferenceTagger, untagAllTsFiles} from '../../shims';
 import {expectCompleteReuse, makeProgram} from '../../testing';
 import {OptimizeFor} from '../api';
 
@@ -64,9 +64,89 @@ runInEachFileSystem(() => {
 
       expectCompleteReuse(programStrategy.getProgram());
     });
+
+    it('should retain shim tags on shared SourceFiles after updateFiles', () => {
+      assertShimTagsRetainedAfterUpdate(UpdateMode.Complete);
+    });
+
+    it('should retain shim tags on shared SourceFiles after incremental updateFiles', () => {
+      const {program, host, options, typecheckPath, mainPath} =
+        makeProgramWhereShimIsIncludedViaReference();
+
+      const programStrategy = new TsCreateProgramDriver(program, host, options, ['ngtypecheck']);
+
+      programStrategy.updateFiles(
+        new Map([[typecheckPath, createUpdate('export const VERSION = 2;')]]),
+        UpdateMode.Complete,
+      );
+      programStrategy.updateFiles(
+        new Map([[typecheckPath, createUpdate('export const VERSION = 3;')]]),
+        UpdateMode.Incremental,
+      );
+
+      assertSharedSourceFileShimTags(programStrategy.getProgram(), mainPath);
+    });
+
+    it('should allow untagging the input program for emit after updateFiles', () => {
+      const {program, host, options, typecheckPath, mainPath} =
+        makeProgramWhereShimIsIncludedViaReference();
+
+      const programStrategy = new TsCreateProgramDriver(program, host, options, ['ngtypecheck']);
+
+      // Update only the shim file so /main.ts remains a shared SourceFile between programs.
+      programStrategy.updateFiles(
+        new Map([[typecheckPath, createUpdate('export const VERSION = 2;')]]),
+        UpdateMode.Complete,
+      );
+
+      const mainSf = getSourceFileOrError(program, mainPath);
+      const ext = sfExtensionData(mainSf);
+
+      expect(ext.taggedReferenceFiles).not.toBeNull();
+      expect(mainSf.referencedFiles.length).toEqual(ext.taggedReferenceFiles!.length);
+
+      // prepareEmit() untags the input program before emit (#56945).
+      untagAllTsFiles(program);
+
+      expect(ext.originalReferencedFiles).not.toBeNull();
+      expect(mainSf.referencedFiles).toEqual(ext.originalReferencedFiles!);
+      for (const ref of mainSf.referencedFiles) {
+        expect(ref.fileName).not.toContain('ngtypecheck');
+      }
+    });
   });
 });
 
+function assertShimTagsRetainedAfterUpdate(updateMode: UpdateMode): void {
+  const {program, host, options, typecheckPath, mainPath} =
+    makeProgramWhereShimIsIncludedViaReference();
+
+  const programStrategy = new TsCreateProgramDriver(program, host, options, ['ngtypecheck']);
+
+  // Update only the shim file so /main.ts remains a shared SourceFile between programs.
+  programStrategy.updateFiles(
+    new Map([[typecheckPath, createUpdate('export const VERSION = 2;')]]),
+    updateMode,
+  );
+
+  assertSharedSourceFileShimTags(programStrategy.getProgram(), mainPath);
+}
+
+function assertSharedSourceFileShimTags(program: ts.Program, mainPath: AbsoluteFsPath): void {
+  const mainSf = getSourceFileOrError(program, mainPath);
+  const ext = sfExtensionData(mainSf);
+
+  // Without the fix, untagging the old program also untags shared SourceFiles in the new
+  // program, leaving referencedFiles shorter than taggedReferenceFiles.
+  expect(ext.taggedReferenceFiles).not.toBeNull();
+  expect(mainSf.referencedFiles.length).toEqual(ext.taggedReferenceFiles!.length);
+
+  // Replicates the TS 5.5+ crash from #68164: with composite, a shim included only via
+  // referencedFiles gets a lazy "not listed in project" diagnostic. Expanding that diagnostic
+  // walks the ReferenceFile include reason and reads main.referencedFiles[index].
+  expect(() => program.getSemanticDiagnostics(mainSf)).not.toThrow();
+}
+
 function createUpdate(text: string): FileUpdate {
   return {
     newText: text,
@@ -116,3 +196,76 @@ function makeSingleFileProgramWithTypecheckShim(): {
 
   return {program, host, options, mainPath, typecheckPath};
 }
+
+/**
+ * Build a program where the ngtypecheck shim is pulled in only through a tagged
+ * `referencedFiles` entry (not as a root). Combined with `composite`, TypeScript records a lazy
+ * project-file-list diagnostic whose expansion exercises `referencedFiles[index]` — the path that
+ * crashes when shared SourceFiles are untagged after `updateFiles()`.
+ */
+function makeProgramWhereShimIsIncludedViaReference(): {
+  program: ts.Program;
+  host: ts.CompilerHost;
+  options: ts.CompilerOptions;
+  mainPath: AbsoluteFsPath;
+  typecheckPath: AbsoluteFsPath;
+} {
+  const mainPath = absoluteFrom('/main.ts');
+  const typecheckPath = absoluteFrom('/main.ngtypecheck.ts');
+  const {host, options} = makeProgram(
+    [
+      {
+        name: mainPath,
+        contents: 'export const NOT_A_COMPONENT = true;',
+      },
+      {
+        name: typecheckPath,
+        contents: 'export const VERSION = 1;',
+        isRoot: false,
+      },
+    ],
+    {
+      composite: true,
+      declaration: true,
+    },
+    /* host */ undefined,
+    /* checkForErrors */ false,
+  );
+
+  const shimTagger = new ShimReferenceTagger(['ngtypecheck']);
+  // Inherit prototype methods from the real host; object spread would drop them.
+  const taggingHost = Object.create(host) as ts.CompilerHost;
+  taggingHost.getSourceFile = (
+    fileName: string,
+    languageVersionOrOptions: ts.ScriptTarget | ts.CreateSourceFileOptions,
+    onError?: (message: string) => void,
+    shouldCreateNewSourceFile?: boolean,
+  ): ts.SourceFile | undefined => {
+    const sf = host.getSourceFile(
+      fileName,
+      languageVersionOrOptions,
+      onError,
+      shouldCreateNewSourceFile,
+    );
+    if (sf !== undefined) {
+      shimTagger.tag(sf);
+    }
+    return sf;
+  };
+
+  const program = ts.createProgram({
+    rootNames: [host.getCanonicalFileName(mainPath)],
+    options,
+    host: taggingHost,
+  });
+  shimTagger.finalize();
+
+  const typecheckSf = getSourceFileOrError(program, typecheckPath);
+  sfExtensionData(typecheckSf).fileShim = {
+    extension: 'ngtypecheck',
+    generatedFrom: mainPath,
+  };
+
+  // Return the unwrapped host; TsCreateProgramDriver installs its own tagging host on updates.
+  return {program, host, options, mainPath, typecheckPath};
+}