I have now tested this a bit and it does seem to be related to some Thursday night clean up. For me it wasn't always the same time when testing several times but my Sims family disappeared on Thursday Night between 3-6 am.
The wife was pregnant and they had a son, all gone. It isn't just families though but they seem most vulnerable. I need to do some more testing but since it's reproducible I hope that the devs can check what routine runs Thursday night that could potentially be responsible for this.
The only work around I see at this point is to save on wednesday under a new name and then see what families disappear. Play those you wanna keep (although you can only save one).
This is most definitly is game breaking and I hope EA finds the cause and can fix it.