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);