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
@@ -800,6 +800,12 @@
     return Count;
   }
 
+  // Remove all call site samples for inlinees. This is needed when flattening
+  // a nested profile.
+  void removeAllCallsiteSamples() {
+    CallsiteSamples.clear();
+  }
+
   // Accumulate all call target samples to update the body samples.
   void updateCallsiteSamples() {
     for (auto &I : BodySamples) {
@@ -957,8 +963,6 @@
     return CallsiteSamples;
   }
 
-  CallsiteSampleMap &getCallsiteSamples() { return CallsiteSamples; }
-
   /// Return the maximum of sample counts in a function body. When SkipCallSite
   /// is false, which is the default, the return count includes samples in the
   /// inlined functions. When SkipCallSite is true, the return count only
@@ -1384,9 +1388,9 @@
     auto Ret = OutputProfiles.try_emplace(Context, FS);
     FunctionSamples &Profile = Ret.first->second;
     if (Ret.second) {
-      // When it's the copy of the old profile, just clear all the inlinees'
-      // samples.
-      Profile.getCallsiteSamples().clear();
+      // Clear nested inlinees' samples for the flattened copy. These inlinees
+      // will have their own top-level entries after flattening.
+      Profile.removeAllCallsiteSamples();
       // We recompute TotalSamples later, so here set to zero.
       Profile.setTotalSamples(0);
     } else {