Set the files found during node_modules search correctly when reusing existing program structure

This marks files reused correctly as from external library resulting in not using them for files to be emitted and computed for output structure
Fixes #19327

src/compiler/program.ts

@@ -1049,6 +1049,10 @@ namespace ts {
             // update fileName -> file mapping
             for (let i = 0; i < newSourceFiles.length; i++) {
                 filesByName.set(filePaths[i], newSourceFiles[i]);
+                // Set the file as found during node modules search if it was found that way in old progra,
+                if (oldProgram.isSourceFileFromExternalLibrary(oldProgram.getSourceFileByPath(filePaths[i]))) {
+                    sourceFilesFoundSearchingNodeModules.set(filePaths[i], true);
+                }
             }
 
             files = newSourceFiles;

src/harness/unittests/tscWatchMode.ts

@@ -1927,6 +1927,7 @@ declare module "fs" {
             expectedFiles[1].isExpectedToEmit = false;
             host.reloadFS(programFiles.concat(configFile));
             host.runQueuedTimeoutCallbacks();
+            checkProgramActualFiles(watch(), programFiles.map(f => f.path));
             checkOutputErrors(host, emptyArray);
             verifyExpectedFiles(expectedFiles);