diff --git a/tools/bugpoint/Miscompilation.cpp b/tools/bugpoint/Miscompilation.cpp
index 5574303321c..771ec34b73c 100644
--- a/tools/bugpoint/Miscompilation.cpp
+++ b/tools/bugpoint/Miscompilation.cpp
@@ -337,8 +337,13 @@ static bool ExtractLoops(BugDriver &BD,
                                     false, Error, Failure);
     if (!New)
       return false;
+
     // Delete the original and set the new program.
-    delete BD.swapProgramIn(New);
+    Module *Old = BD.swapProgramIn(New);
+    for (unsigned i = 0, e = MiscompiledFunctions.size(); i != e; ++i)
+      MiscompiledFunctions[i] = cast<Function>(VMap[MiscompiledFunctions[i]]);
+    delete Old;
+
     if (Failure) {
       BD.switchToInterpreter(AI);
 
@@ -366,21 +371,51 @@ static bool ExtractLoops(BugDriver &BD,
 
     outs() << "  Testing after loop extraction:\n";
     // Clone modules, the tester function will free them.
-    Module *TOLEBackup = CloneModule(ToOptimizeLoopExtracted);
-    Module *TNOBackup  = CloneModule(ToNotOptimize);
+    Module *TOLEBackup = CloneModule(ToOptimizeLoopExtracted, VMap);
+    Module *TNOBackup  = CloneModule(ToNotOptimize, VMap);
+
+    for (unsigned i = 0, e = MiscompiledFunctions.size(); i != e; ++i)
+      MiscompiledFunctions[i] = cast<Function>(VMap[MiscompiledFunctions[i]]);
+
     Failure = TestFn(BD, ToOptimizeLoopExtracted, ToNotOptimize, Error);
     if (!Error.empty())
       return false;
+
+    ToOptimizeLoopExtracted = TOLEBackup;
+    ToNotOptimize = TNOBackup;
+
     if (!Failure) {
       outs() << "*** Loop extraction masked the problem.  Undoing.\n";
       // If the program is not still broken, then loop extraction did something
       // that masked the error.  Stop loop extraction now.
-      delete TOLEBackup;
-      delete TNOBackup;
+
+      std::vector<std::pair<std::string, FunctionType*> > MisCompFunctions;
+      for (unsigned i = 0, e = MiscompiledFunctions.size(); i != e; ++i) {
+        Function *F = MiscompiledFunctions[i];
+        MisCompFunctions.push_back(std::make_pair(F->getName(),
+                                                  F->getFunctionType()));
+      }
+
+      std::string ErrorMsg;
+      if (Linker::LinkModules(ToNotOptimize, ToOptimizeLoopExtracted, 
+                              Linker::DestroySource, &ErrorMsg)){
+        errs() << BD.getToolName() << ": Error linking modules together:"
+               << ErrorMsg << '\n';
+        exit(1);
+      }
+
+      MiscompiledFunctions.clear();
+      for (unsigned i = 0, e = MisCompFunctions.size(); i != e; ++i) {
+        Function *NewF = ToNotOptimize->getFunction(MisCompFunctions[i].first);
+
+        assert(NewF && "Function not found??");
+        MiscompiledFunctions.push_back(NewF);
+      }
+
+      delete ToOptimizeLoopExtracted;
+      BD.setNewProgram(ToNotOptimize);
       return MadeChange;
     }
-    ToOptimizeLoopExtracted = TOLEBackup;
-    ToNotOptimize = TNOBackup;
 
     outs() << "*** Loop extraction successful!\n";