This sounds like expected EA behavior with Story Progression enabled. Unless you have the AwesomeMod and have configured it correctly, the game will arbitrarily remove your sims.
Yeah, I have Awesomemod and have all the "No Bus" stuff enabled, so I'm not sure what's up. I hate not having Cornelia Goth's gravestone in the little Goth cemetery. I'm debating making another Cornelia Goth and killing her but I'm not sure if that will mess stuff up.