Index: lib/Frontend/CompilerInstance.cpp
===================================================================
--- lib/Frontend/CompilerInstance.cpp
+++ lib/Frontend/CompilerInstance.cpp
@@ -374,7 +374,14 @@
   // The module manager holds a reference to the old preprocessor (if any).
   ModuleManager.reset();
 
-  // Create the Preprocessor.
+  // Create the Preprocessor. If this instance is replacing the existing
+  // preprocessor and that existing one is going away, we have to remove
+  // the Module* pointers it owns from KnownModules since they will be
+  // dangling. FIXME: Should this only remove pointers owned by the
+  // preprocessor that is going away or clear the entire map (or can
+  // the map even own any other Module* pointers)?
+  if (PP.unique())
+    KnownModules.clear();
   HeaderSearch *HeaderInfo =
       new HeaderSearch(getHeaderSearchOptsPtr(), getSourceManager(),
                        getDiagnostics(), getLangOpts(), &getTarget());