I know this is an older thread, but something I recently noticed when I came back to playing my game
Outdated/obsolete CC/Mods caused some of my sims to disappear - Once I removed the CC that was causing the issue, my missing sims returned and haven't been a problem since! It took a bit of trial and error to find the actual content that was the source of the problem, but a couple of reloads of a older save meant that I was able to resolve the issue and bring back the missing sims!
I posted about it on this thread
forums.thesims.com/en_US/discussion/918053/outdated-cc-caused-active-sims-to-vanish-from-household-resolved-and-they-are-back#latest