diff --git a/src/index.ts b/src/index.ts
index 1d5351b5f..48d4c21ea 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -358,6 +358,20 @@ function updateFileInCache(
     fileWatcherEventKind = instance.compiler.FileWatcherEventKind.Deleted;
   }
 
+  // filePath is a root file as it was passed to the loader. But it
+  // could have been found earlier as a dependency of another file. If
+  // that is the case, compiling this file changes the structure of
+  // the program and we need to increase the instance version.
+  //
+  // See https://github.com/TypeStrong/ts-loader/issues/943
+  if (
+    !instance.rootFileNames.has(filePath) &&
+    filePath.indexOf('node_modules') === -1
+  ) {
+    instance.version!++;
+    instance.rootFileNames.add(filePath);
+  }
+
   if (file.text !== contents) {
     file.version++;
     file.text = contents;
@@ -381,6 +395,7 @@ function updateFileInCache(
     instance.modifiedFiles = new Map<string, TSFile>();
   }
   instance.modifiedFiles.set(filePath, file);
+
   return file.version;
 }
 
diff --git a/src/instances.ts b/src/instances.ts
index c745687b3..1d436f2a1 100644
--- a/src/instances.ts
+++ b/src/instances.ts
@@ -124,6 +124,7 @@ function successfulTypeScriptInstance(
   }
 
   const compilerOptions = getCompilerOptions(configParseResult);
+  const rootFileNames = new Set<string>();
   const files: TSFiles = new Map<string, TSFile>();
   const otherFiles: TSFiles = new Map<string, TSFile>();
 
@@ -199,6 +200,7 @@ function successfulTypeScriptInstance(
       compilerOptions,
       appendTsTsxSuffixesIfRequired,
       loaderOptions,
+      rootFileNames,
       files,
       otherFiles,
       program,
@@ -225,6 +227,7 @@ function successfulTypeScriptInstance(
         text: fs.readFileSync(normalizedFilePath, 'utf-8'),
         version: 0
       });
+      rootFileNames.add(normalizedFilePath);
     });
   } catch (exc) {
     return {
@@ -248,6 +251,7 @@ function successfulTypeScriptInstance(
     compilerOptions,
     appendTsTsxSuffixesIfRequired,
     loaderOptions,
+    rootFileNames,
     files,
     otherFiles,
     languageService: null,
diff --git a/src/interfaces.ts b/src/interfaces.ts
index f5de787fe..0f2deb7bd 100644
--- a/src/interfaces.ts
+++ b/src/interfaces.ts
@@ -55,6 +55,7 @@ export interface TSInstance {
   /** Used for Vue for the most part */
   appendTsTsxSuffixesIfRequired: (filePath: string) => string;
   loaderOptions: LoaderOptions;
+  rootFileNames: Set<string>;
   /**
    * a cache of all the files
    */