Several sims on my save files family tree keep turning into "Unknown Sims", after not being in my currently played household anymore. This means that connected sims (like children) are also subsequently removed from the complete tree, as the link between them no longer exists. Both sims that have been played directly (previously a child in my household which was left alone once grown) and not touched at all (apart from creating a child with another sim in CAS) has been affected by this.
I have not deleted them myself, they just suddenly converted into "Unknown Sim" in the family tree.