Partnered Sims turn into siblings

I've been playing in a generation household for years, and for some reason my sims keep getting marked as related??

I have MC Command Center, so I went in and manually removed the "brothers" relationship bit from both sims (even removed the "family dynamic" just in case that was causing issues) and added back the "partner" relationship bit. Their romance bar showed up again, as well as a "romantic satisfaction" popup from lovestruck, but the romantic interactions are still restricted to "offer massage" and "make a move."

Going into their simology, I can see that the game thinks they share the same mother for some reason (even after messing with the relationship bits). Sim A has the correct mother assigned, but Sim B does not. I have tried to reassign Sim B's mother, but the simology doesn't update. 

I've tried looking for the mother in the unplayed households, but I can't find her. She became a ghost before Life and Death (not sure if that's relevant or not) and she doesn't even show up in the list of sims that either sim knows. When I try to add a relationship with "sim in world" she still doesn't show up on that list either. I don't have a headstone for her since all the data for my household headstones got wiped when I installed Life and Death and stored them in a crypt. (I tried going back to old versions of the lot saved to the gallery, but those are wiped as well.

I have no idea how to find this "mother" sim and edit her or at the very least delete her, it seems like it's so deep in the meta data for the game that trying to fix this is out of my depth, please help!