I have a similar or maybe even the same issue.
When I enter CAS and save changes, the relationship to one parent is changed to uncle/aunt. The game creates an unknown parent in the family tree. I tested this with and completely without mods. Even without mods, the bug kept happening after entering CAS and saving the changes. I have a big file with many households with many family relations connecting them (5th generation). I usually fix the relationship via MCCC, but my sim forgets every trait of their parent in the process. And I have to exit and reenter the household for the family tree to be fixed. The unknown proxy parent stays in the family tree as an uncle/aunt which doesn't look great in the family tree. It's really annoying, I even transfered all my sims to a new save, re-established every relationship from scratch from the first generation on (brought them back to life and killed them off again), just to find out, the bug happens everytime I enter and exit CAS.
Interesting. So far I haven't noticed any faceless family members, but I haven't looked through all my households yet. I tried using MCCC as well to fix the issue, but even after doing it the broken family relationships remained. I plan to try a new save to see what happens, but I am hoping it ends up being fixable since this is the save file I've had since first getting thr game.
