diff --git a/include/swift/SIL/SILProfiler.h b/include/swift/SIL/SILProfiler.h
index 45ab785cae1d6..c7cfb3b595860 100644
--- a/include/swift/SIL/SILProfiler.h
+++ b/include/swift/SIL/SILProfiler.h
@@ -93,9 +93,6 @@ class SILProfiler : public SILAllocated<SILProfiler> {
     return RegionCounterMap;
   }
 
-  /// Increment the number of counter updates associated with this profiler.
-  void recordCounterUpdate();
-
 private:
   /// Map counters to ASTNodes and set them up for profiling the function.
   void assignRegionCounters();
diff --git a/lib/IRGen/GenBuiltin.cpp b/lib/IRGen/GenBuiltin.cpp
index 66b3d9b1f6f01..c176966981eb7 100644
--- a/lib/IRGen/GenBuiltin.cpp
+++ b/lib/IRGen/GenBuiltin.cpp
@@ -206,7 +206,9 @@ void irgen::emitBuiltinCall(IRGenFunction &IGF, const BuiltinInfo &Builtin,
   if (IID == llvm::Intrinsic::instrprof_increment) {
     // If we import profiling intrinsics from a swift module but profiling is
     // not enabled, ignore the increment.
-    if (!IGF.getSILModule().getOptions().GenerateProfile) {
+    SILModule &SILMod = IGF.getSILModule();
+    const auto &Opts = SILMod.getOptions();
+    if (!Opts.GenerateProfile) {
       (void)args.claimAll();
       return;
     }
@@ -246,6 +248,15 @@ void irgen::emitBuiltinCall(IRGenFunction &IGF, const BuiltinInfo &Builtin,
     replacement.add(NameGEP);
     replacement.add(args.claimAll());
     args = std::move(replacement);
+
+    if (Opts.EmitProfileCoverageMapping) {
+      // Update the associated coverage mapping: it's now safe to emit, because
+      // a symtab entry for this function is guaranteed (r://39146527).
+      auto &coverageMaps = SILMod.getCoverageMaps();
+      auto CovMapIt = coverageMaps.find(PGOFuncName);
+      if (CovMapIt != coverageMaps.end())
+        CovMapIt->second->setSymtabEntryGuaranteed();
+    }
   }
 
   if (IID != llvm::Intrinsic::not_intrinsic) {
diff --git a/lib/IRGen/GenDecl.cpp b/lib/IRGen/GenDecl.cpp
index 653bfdcc935ff..856530b056e1e 100644
--- a/lib/IRGen/GenDecl.cpp
+++ b/lib/IRGen/GenDecl.cpp
@@ -1065,7 +1065,6 @@ void IRGenerator::emitGlobalTopLevel(bool emitForParallelEmission) {
     CurrentIGMPtr IGM = getGenModule(decl ? decl->getDeclContext() : nullptr);
     IGM->emitSILGlobalVariable(&v);
   }
-  PrimaryIGM->emitCoverageMapping();
   
   // Emit SIL functions.
   for (SILFunction &f : PrimaryIGM->getSILModule()) {
@@ -1099,6 +1098,9 @@ void IRGenerator::emitGlobalTopLevel(bool emitForParallelEmission) {
     IGM->emitSILProperty(&prop);
   }
   
+  // Emit code coverage mapping data.
+  PrimaryIGM->emitCoverageMapping();
+
   for (auto Iter : *this) {
     IRGenModule *IGM = Iter.second;
     IGM->finishEmitAfterTopLevel();
diff --git a/lib/SIL/SILProfiler.cpp b/lib/SIL/SILProfiler.cpp
index ca8e18ed5d948..d00e16539c7d2 100644
--- a/lib/SIL/SILProfiler.cpp
+++ b/lib/SIL/SILProfiler.cpp
@@ -1081,10 +1081,3 @@ Optional<ASTNode> SILProfiler::getPGOParent(ASTNode Node) {
   }
   return it->getSecond();
 }
-
-void SILProfiler::recordCounterUpdate() {
-  // If a counter update is recorded, the profile symbol table is guaranteed
-  // to have name data needed by the coverage mapping.
-  if (CovMap)
-    CovMap->setSymtabEntryGuaranteed();
-}
diff --git a/lib/SILGen/SILGenFunction.cpp b/lib/SILGen/SILGenFunction.cpp
index 8f9885ded9490..022dea0b84863 100644
--- a/lib/SILGen/SILGenFunction.cpp
+++ b/lib/SILGen/SILGenFunction.cpp
@@ -658,7 +658,6 @@ void SILGenFunction::emitProfilerIncrement(ASTNode N) {
       B.createIntegerLiteral(Loc, Int32Ty, CounterIt->second)};
   B.createBuiltin(Loc, C.getIdentifier("int_instrprof_increment"),
                   SGM.Types.getEmptyTupleType(), {}, Args);
-  SP->recordCounterUpdate();
 }
 
 ProfileCounter SILGenFunction::loadProfilerCount(ASTNode Node) const {