Sim died, but why was she deleted from the game?

If she was in a played household I would guess a bug. If not, then I would guess culling. Culling should only happen to unplayed households, and with ghosts you don't strengthen a connection to.

Here is a guide on culling if you want to understand it better. I was seriously confused about it and as a rotational player, I found it a bit stressful, until someone showed me this:
https://sims4.crinrict.com/eng/2016/06/culling-what-is-it-and-what-does-it-do/