diff --git a/llvm/include/llvm/ProfileData/SampleProf.h b/llvm/include/llvm/ProfileData/SampleProf.h
--- a/llvm/include/llvm/ProfileData/SampleProf.h
+++ b/llvm/include/llvm/ProfileData/SampleProf.h
@@ -1603,10 +1603,22 @@
                            ? TotalSamples - CalleeProfile.getTotalSamples()
                            : 0;
         TotalSamples += CalleeProfile.getHeadSamplesEstimate();
+
+      }
+    }
+
+    // FlattenNestedProfile adds new FunctionSamples to the output, which may
+    // invalidate the reference Profile, so it needs to be reset after all
+    // flattening.
+    for (const auto &I : FS.getCallsiteSamples()) {
+      for (const auto &Callee : I.second) {
+        const auto &CalleeProfile = Callee.second;
         // Recursively convert callee profile.
         flattenNestedProfile(OutputProfiles, CalleeProfile);
       }
     }
+    Profile = OutputProfiles[Context];
+
     Profile.addTotalSamples(TotalSamples);
 
     Profile.setHeadSamples(Profile.getHeadSamplesEstimate());