I have had this happen before and it just happened again.
I don't know why it happened exactly but just realized that there is one common thing in those two situations.

I recently moved a group of sims to another world. In that group, I have single sims and some of them left their siblings in the world A.
It only happened to a sim that has a deceased sibling left in the world A. The family tree of that moved sim in the world B was ok. But her dad and mom were still in the world A. I recently went back to world A and found that her mom and dad's family trees were messed up... I did fix homeworld and everything that was on the instruction but nothing helped.

Now I remember last time when it had happened, it was the same situation. One of my sims who had deceased siblings moved to another world and the rest of the family members left in the original world had broken family trees.

I'm not sure if it's all random but thought it would be good to share..

Did you use the game's method of moving sims? Nraas has the Porter mod which allows you to ship sims between worlds, so perhaps you could try it? See if you can test it out using a an earlier Save before the move?

The genealogy system is complex and easy to break. But what do you mean when you say messed up? What was unexpected or missing?

There were four 6 members in the family. Young son was a child when he died. I moved three sisters to a different world and then I came back to this world. In those father’s and mother’s family tree, one of those sisters is missing. Then, i clicked one of those sisters portrait in the parent’s family tree, all four siblings are shown but the lines are all disconnected.

I actually solved this problem. I was going through MC>Sim>Basic>Family tree>Homeworld>the world where those sisters live> then i found that, one of those sisters, there are two same sims with different ages. It seems that's causing this problem. I don’t know if it has something to do with having a deceased sibling though like I wrote above. Just to check, I went to the other world where sisters are living but there, it was ok. No doppelganger sims. So from there, I came back to the original world but the family tree was still broken.
So this time, I remember that one of the nrass mod have the feature of deleting doppelganger sims when the game is loaded. So I invite that problematic daughter and her doppelganger using MC>invite over. I got a message saying that she will come soon for both of those sims but only one visited. So as soon as she arrived, i saved the game, quit and reload. The family tree was fixed for everyone in that family and I sent her back to her world.