Index: lib/fuzzer/FuzzerLoop.cpp
===================================================================
--- lib/fuzzer/FuzzerLoop.cpp
+++ lib/fuzzer/FuzzerLoop.cpp
@@ -466,16 +466,11 @@
 
   // First Rerun
   CBSetupAndRun();
-  TPC.UpdateUnstableCounters(Options.HandleUnstable);
-
-  // Second Rerun
-  CBSetupAndRun();
-  TPC.UpdateUnstableCounters(Options.HandleUnstable);
-
-  // Move minimum hit counts back to ModuleInline8bitCounters
-  if (Options.HandleUnstable == TracePC::MinUnstable ||
-      Options.HandleUnstable == TracePC::ZeroUnstable)
-    TPC.ApplyUnstableCounters();
+  if (TPC.UpdateUnstableCounters(Options.HandleUnstable)) {
+    // Second Rerun
+    CBSetupAndRun();
+    TPC.UpdateAndApplyUnstableCounters(Options.HandleUnstable);
+  }
 }
 
 bool Fuzzer::RunOne(const uint8_t *Data, size_t Size, bool MayDeleteFile,
Index: lib/fuzzer/FuzzerTracePC.h
===================================================================
--- lib/fuzzer/FuzzerTracePC.h
+++ lib/fuzzer/FuzzerTracePC.h
@@ -143,8 +143,8 @@
   bool ObservedFocusFunction();
 
   void InitializeUnstableCounters();
-  void UpdateUnstableCounters(int UnstableMode);
-  void ApplyUnstableCounters();
+  bool UpdateUnstableCounters(int UnstableMode);
+  void UpdateAndApplyUnstableCounters(int UnstableMode);
 
 private:
   struct UnstableEdge {
Index: lib/fuzzer/FuzzerTracePC.cpp
===================================================================
--- lib/fuzzer/FuzzerTracePC.cpp
+++ lib/fuzzer/FuzzerTracePC.cpp
@@ -81,9 +81,11 @@
 
 // Compares the current counters with counters from previous runs
 // and records differences as unstable edges.
-void TracePC::UpdateUnstableCounters(int UnstableMode) {
+bool TracePC::UpdateUnstableCounters(int UnstableMode) {
+  bool Updated = false;
   IterateInline8bitCounters([&](int i, int j, int UnstableIdx) {
     if (ModuleCounters[i].Start[j] != UnstableCounters[UnstableIdx].Counter) {
+      Updated = true;
       UnstableCounters[UnstableIdx].IsUnstable = true;
       if (UnstableMode == ZeroUnstable)
         UnstableCounters[UnstableIdx].Counter = 0;
@@ -92,12 +94,20 @@
             ModuleCounters[i].Start[j], UnstableCounters[UnstableIdx].Counter);
     }
   });
+  return Updated;
 }
 
-// Moves the minimum hit counts to ModuleCounters.
-void TracePC::ApplyUnstableCounters() {
+// Updates and applies unstable counters to ModuleCounters in single iteration
+void TracePC::UpdateAndApplyUnstableCounters(int UnstableMode) {
   IterateInline8bitCounters([&](int i, int j, int UnstableIdx) {
-    ModuleCounters[i].Start[j] = UnstableCounters[UnstableIdx].Counter;
+    if (ModuleCounters[i].Start[j] != UnstableCounters[UnstableIdx].Counter) {
+      UnstableCounters[UnstableIdx].IsUnstable = true;
+      if (UnstableMode == ZeroUnstable)
+        ModuleCounters[i].Start[j] = 0;
+      else if (UnstableMode == MinUnstable)
+        ModuleCounters[i].Start[j] = std::min(
+            ModuleCounters[i].Start[j], UnstableCounters[UnstableIdx].Counter);
+    }
   });
 }