@SimGuruLindsay, there are several threads on this topic and I've been tracking them. I think there are multiple issues here, but I'm convinced that most of these disappearances are related to saving/loading practices.
Where to start ...
Okay, first, people who follow these steps do not seem to be having the problem: Use "Save As" rather than "Save"; always "Save As" and then exit (never "save and exit"); always Save As on the family's home lot (not a public venue); always load the game from the saved games accessed by clicking the icon at the top right of the loading screen (rather than clicking the "play" arrow at the lower right); always choose the most recently saved game (unless you want to go back to a point in time); NEVER load the autosave.
- No one understands how autosave works. When you looked at the saved games to load, there is always only one autosave, and it is time-stamped at the time of your last save/save as. There are not multiple autosaves accessible where you could go back in time to a certain restore point (although there appear to be multiple autosaves in the Saves folder). When I've experimented with loading the autosave, it's never quite where I left off; things are slightly different. I haven't lost any Sims. However, I notice when I experiment with loading from the play button, it seems like it is loading the autosave and not my last "Save as" game.
- I think some people who use Save As don't understand how that works. The Save As always associates the name of the family you were playing with the save. I think that some people, when they've played another family and want to go back to the original family, are going back to old saves associated with that name. There would be an understandable disappearance of Sims/progress in cases like that.
- I'm not sure everyone understands the aging settings. For whatever reason, I know when I first got the game I did not see the "Active household only" aging function. I just saw "no aging" or "aging for played families." When using the latter, any family you've played, even for a minute, keeps aging. Sims grow old and die. I know, theoretically they should still be in the relationship panel, unless the game is releasing their spirits to the other world by default.
Anyway, those are my thoughts. I follow the saving/loading procedure I outlined. I have aging set to the Active Family Only, and unplayed Sims set on no aging. I'm playing multiple families and haven't lost anyone (yet, knock wood).
I may be totally off base, but I'm hoping that maybe it will give a direction to look.