Bumping again. Issue persists in Unreal 5.0 May 2022. Really annoying, it should be able to clean things up for itself, or at least communicate more clearly to the user. This is a UX issue for sure even if it isn’t an actual “engine” issue.
The tip about recognizing whether they are “real” references or just old memory was helpful but still way more confusing then it should be (like spending 15 minutes reading this forum just to delete a single file).