When a sim is dead I noticed that in their portrait the background turns blue. After installing the cleaned up templates when I kill off a Sims their portrait background stays the normal grey.
The blue background should be IIRC about "unlinked" state (default for Maxis' dead sims). There's a hack by Pescado which prevents dead sims unlinkage, maybe you have that hack too.
In any case, though, it should not be a bad thing for your sims.
It didn't bother me as it seemed not to be causing any game issues, but when playing today one of my teens came home I got the pop up that he had brought home a friend and it was one of the teens I had killed off. As soon as he got off the bus a second pop up came up saying that she had died on another lot and will return to that lot. I'm guessing something is screwy.
This is the regular behavior; probably you saved the lot before with that teen already scheduled as a brought-home schoolmate. In those cases the game loads the now-dead sim and process it exactly the way you witnessed.
I also now have duplicates of Skip and darlenn (if that's her name) it doesn't bother me, just wanted to make sure I didn't do something wrong or it will cause problems.
Yet another regular feature of default Pleasantview: the game ships with duplicates of Skip Broke, Darleen Dreamer, and IIRC also other dead sims. It's not your fault
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