Hello guys! So I'm working on a custom hood for Sims 2 these days and for some reason my sims keep losing their character data. I tried to fix this with hood checker but no problem was found.
These Sims are perfectly fine in-game, but for some reason SimPE says they don't have character data. 'Cause I plan to make this hood available for download in the future I need it to be perfect! Does anybody know how to fix it or what causes this?

Some info:
I used InSimenator to create family trees, and for each Sim alive there's at least 6 dead Sims (as ancestors of the living Sim). I do believe this can be somewhat related to the problem, 'cause sometimes the Sims would lose their Character Data while I was creating family ties with InSimenator.
I do have tons of backups here and one where no one lost their character data, but all family ties were already set.

Their characters are intact, but I noticed there's two characters files missing (242, 243) although there's no Sim with these numbers, so I'm not even sure this is a problem at all.

Anybody knows what's going on?

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You're likely running into split character files - do you see any files in the Characters folder with a .1 before the extension? Everything is still there, but since SimPE isn't aware of split files it'll report missing data.