First of all make sure everything's lit. Other than that, IME if there's any way they can inflict fall damage on themselves, they will keep jumping off there, and maybe even die eventually. Or if you have their beds in weird positions, they might be able to escape confinement or get out of bed into a wall and suffocate.
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makes sense actually
If it's on the surface, you can get lightning strikes that turn villagers into witches, which them despawn.
but i have lightning rods and the villagers are covered
Also, you bedrock or Java? Bedrock has had the issue before of just vanishing entities, I don't know if it's fully fixed.
on java
Have you used an ID tag on them to prevent despawning?
i actually tried that (even tho they dont despawn) and it did nothing
I haven't had them despawn but I have had them lose all their trades and levels because I was gone so long.