diff --git a/llvm/include/llvm/Transforms/Scalar/LoopPassManager.h b/llvm/include/llvm/Transforms/Scalar/LoopPassManager.h
--- a/llvm/include/llvm/Transforms/Scalar/LoopPassManager.h
+++ b/llvm/include/llvm/Transforms/Scalar/LoopPassManager.h
@@ -281,8 +281,6 @@
   /// state, this routine will mark that the current loop should be skipped by
   /// the rest of the pass management infrastructure.
   void markLoopAsDeleted(Loop &L, llvm::StringRef Name) {
-    assert((!LoopNestMode || CurrentL == &L) &&
-           "L should be a top-level loop in loop-nest mode.");
     LAM.clear(L, Name);
     assert((&L == CurrentL || CurrentL->contains(&L)) &&
            "Cannot delete a loop outside of the "
diff --git a/llvm/lib/Transforms/Scalar/LoopFlatten.cpp b/llvm/lib/Transforms/Scalar/LoopFlatten.cpp
--- a/llvm/lib/Transforms/Scalar/LoopFlatten.cpp
+++ b/llvm/lib/Transforms/Scalar/LoopFlatten.cpp
@@ -606,7 +606,7 @@
 
 static bool DoFlattenLoopPair(FlattenInfo &FI, DominatorTree *DT, LoopInfo *LI,
                               ScalarEvolution *SE, AssumptionCache *AC,
-                              const TargetTransformInfo *TTI) {
+                              const TargetTransformInfo *TTI, LPMUpdater *U) {
   Function *F = FI.OuterLoop->getHeader()->getParent();
   LLVM_DEBUG(dbgs() << "Checks all passed, doing the transformation\n");
   {
@@ -662,6 +662,8 @@
   // deleted, and any information that have about the outer loop invalidated.
   SE->forgetLoop(FI.OuterLoop);
   SE->forgetLoop(FI.InnerLoop);
+  if (U)
+    U->markLoopAsDeleted(*FI.InnerLoop, FI.InnerLoop->getName());
   LI->erase(FI.InnerLoop);
 
   // Increment statistic value.
@@ -737,7 +739,7 @@
 
 static bool FlattenLoopPair(FlattenInfo &FI, DominatorTree *DT, LoopInfo *LI,
                             ScalarEvolution *SE, AssumptionCache *AC,
-                            const TargetTransformInfo *TTI) {
+                            const TargetTransformInfo *TTI, LPMUpdater *U) {
   LLVM_DEBUG(
       dbgs() << "Loop flattening running on outer loop "
              << FI.OuterLoop->getHeader()->getName() << " and inner loop "
@@ -766,7 +768,7 @@
 
   // If we have widened and can perform the transformation, do that here.
   if (CanFlatten)
-    return DoFlattenLoopPair(FI, DT, LI, SE, AC, TTI);
+    return DoFlattenLoopPair(FI, DT, LI, SE, AC, TTI, U);
 
   // Otherwise, if we haven't widened the IV, check if the new iteration
   // variable might overflow. In this case, we need to version the loop, and
@@ -784,18 +786,18 @@
   }
 
   LLVM_DEBUG(dbgs() << "Multiply cannot overflow, modifying loop in-place\n");
-  return DoFlattenLoopPair(FI, DT, LI, SE, AC, TTI);
+  return DoFlattenLoopPair(FI, DT, LI, SE, AC, TTI, U);
 }
 
 bool Flatten(LoopNest &LN, DominatorTree *DT, LoopInfo *LI, ScalarEvolution *SE,
-             AssumptionCache *AC, TargetTransformInfo *TTI) {
+             AssumptionCache *AC, TargetTransformInfo *TTI, LPMUpdater *U) {
   bool Changed = false;
   for (Loop *InnerLoop : LN.getLoops()) {
     auto *OuterLoop = InnerLoop->getParentLoop();
     if (!OuterLoop)
       continue;
     FlattenInfo FI(OuterLoop, InnerLoop);
-    Changed |= FlattenLoopPair(FI, DT, LI, SE, AC, TTI);
+    Changed |= FlattenLoopPair(FI, DT, LI, SE, AC, TTI, U);
   }
   return Changed;
 }
@@ -810,7 +812,7 @@
   // in simplified form, and also needs LCSSA. Running
   // this pass will simplify all loops that contain inner loops,
   // regardless of whether anything ends up being flattened.
-  Changed |= Flatten(LN, &AR.DT, &AR.LI, &AR.SE, &AR.AC, &AR.TTI);
+  Changed |= Flatten(LN, &AR.DT, &AR.LI, &AR.SE, &AR.AC, &AR.TTI, &U);
 
   if (!Changed)
     return PreservedAnalyses::all();
@@ -860,7 +862,7 @@
   bool Changed = false;
   for (Loop *L : *LI) {
     auto LN = LoopNest::getLoopNest(*L, *SE);
-    Changed |= Flatten(*LN, DT, LI, SE, AC, TTI);
+    Changed |= Flatten(*LN, DT, LI, SE, AC, TTI, nullptr);
   }
   return Changed;
 }