@: We did get around the crash by toggling that option in the ini file.
We renamed the actors so the map no longer crashes, so I don’t have a handy reproduction for you. I’m not entirely sure how it got into the state. It hasn’t happened a second time (yet?) 
Here’s the call stack. It’s from the previous version.
Fatal error: [File:D:\src\unrealengine\branches\dev\Engine\Source\Runtime\CoreUObject\Private\UObject\Obj.cpp] [Line: 197]
Renaming an object (SpotLight /Game/Maps/Rooms/FRE/Corridors/FRE_CO_4_Circle_A.FRE_CO_4_Circle_A:PersistentLevel.SpotLight_0) on top of an existing object (SpotLight /Game/Maps/Rooms/FRE/Corridors/FRE_CO_4_Circle_A.FRE_CO_4_Circle_A:PersistentLevel.SpotLight_3) is not allowed
UE4Editor_Core!FDebug::AssertFailed() [d:\src\unrealengine\branches\dev\engine\source\runtime\core\private\misc\assertionmacros.cpp:349]
UE4Editor_CoreUObject!UObject::Rename() [d:\src\unrealengine\branches\dev\engine\source\runtime\coreuobject\private\uobject\obj.cpp:197]
UE4Editor_Engine!AActor::Rename() [d:\src\unrealengine\branches\dev\engine\source\runtime\engine\private\actor.cpp:823]
UE4Editor_PrefabAsset!FPrefabToolEditorUtil::ReplacePrefabInstances() [d:\src\endeavor\endeavor\plugins\prefabtool\source\prefabasset\private\prefabtoolhelpers.cpp:1637]
UE4Editor_PrefabAsset!FPrefabToolEditorUtil::RevertPrefabActor() [d:\src\endeavor\endeavor\plugins\prefabtool\source\prefabasset\private\prefabtoolhelpers.cpp:2001]
UE4Editor_PrefabAsset!FPrefabToolEditorUtil::RevertAllPrefabActorsInCurrentLevel() [d:\src\endeavor\endeavor\plugins\prefabtool\source\prefabasset\private\prefabtoolhelpers.cpp:2266]
UE4Editor_PrefabAssetEditor!TBaseRawMethodDelegateInstance<0,FPrefabAssetEditorModule,void __cdecl(FString const & __ptr64,bool)>::ExecuteIfSafe() [d:\src\unrealengine\distrib\engine\source\runtime\core\public\delegates\delegateinstancesimpl.h:648]
UE4Editor_UnrealEd!TBaseMulticastDelegate<void,FString const & __ptr64,bool>::Broadcast() [d:\src\unrealengine\branches\dev\engine\source\runtime\core\public\delegates\delegatesignatureimpl.inl:937]
UE4Editor_UnrealEd!FEditorFileUtils::LoadMap()
The line is
NewActor->Rename(*OldActorName.ToString());