diff --git a/llvm/tools/bugpoint/Miscompilation.cpp b/llvm/tools/bugpoint/Miscompilation.cpp
--- a/llvm/tools/bugpoint/Miscompilation.cpp
+++ b/llvm/tools/bugpoint/Miscompilation.cpp
@@ -591,9 +591,6 @@
   if (Linker::linkModules(*ProgClone, std::move(Extracted)))
     exit(1);
 
-  // Set the new program and delete the old one.
-  BD.setNewProgram(std::move(ProgClone));
-
   // Update the list of miscompiled functions.
   MiscompiledFunctions.clear();
 
@@ -603,6 +600,9 @@
     MiscompiledFunctions.push_back(NewF);
   }
 
+  // Set the new program and delete the old one.
+  BD.setNewProgram(std::move(ProgClone));
+
   return true;
 }