I am unable to reproduce it. I would recommend creating an answerhub post and they may ask you to upload a repro test case.
The steps I mentioned are not some official method or anything, just something I have come to the habit of doing. It is hard to make it into an actual feature or anything since technically when you migrate, everything that comes across IS referenced by the assets you migrate. Usually it is things like default texture that were already overridden by material instances or things like that, so it is kind of expected that you will need to manually replace those references to avoid moving too much content. Or it was some minor component of a blueprint that also brought along all of ITS references. Still it is correct to bring over all that ‘extra’ stuff and the only way to bring over less is to pare it down a little bit. I don’t foresee a tool that can do that automatically since it is subjective what should be considered extra.
You can do that in the original starting project but the reason I use a separate blank project is because many of the operations would be destructive to the original assets and the original project may still need to function.