What’s interesting is that while some of the rooftop level instances can be deleted just fine, the building itself simply cannot be removed.
Are you using Movie Render Queue? I have not heard of something that was deleted come up in a MRQ render. MRQ goes into PIE when it renders. Which means it will run any level logic. Is there any logic that could be loading in that actor?
It may be a part of an HLOD, if you’re using World Partition. In which case, try rebuilding your HLODs and deleting it again if it reappears.