hey, i'm not sure how this messaging thing works bc i've never used it, so i figured it's best to post my response on your wall.
i resolved the family tree issue, but had to basically clone a few of them from my library and set relationships again. the problem seems to occur when siblings are created before the parents, which is what happened in my case. i placed two of the same family from my library into a save, then separated one of the families for cas cloning because my household was too big to merge the clone fam. i can't remember step by step because it was a little while ago now, but i can test it with a random family later and let you know.
of course the risk of this method is losing non familial relationships and skills, so it's up to you, or you can try finding another method. i took the risk bc the broken tree bugged me to no end and it was easier to rebuild their relationships and skills with mccc/cheats. i wish maxis would make the tree easy to edit.