I’m facing the same issue. The interesting part is that I have live coding turned off a while ago and everything was fine. While I modified an BP the Editor crashed and suddenly a lot of my BPs are parentless.
I also recreated a completely new project and the same issues appeared on the exactly same BPs.
Even if I fix the issues manually, after restarting of the Editor, all changes are gone and references lost.
I tried to clear and rebuild project (also removed bin folder) but its not helping.
Hope someone can help me with this problem.