Villagers disappear by sleeping at night.

If you are in the same loaded chunks as the villagers at night, they will go to sleep and fly away through walls even! They will lay down, in that same position, fly in a random direction horizontally. If you are in the same loaded chunks as them, they won't come back in the morning. I have to exit the loaded chunks (for mobs) then return for them to appear back at their beds.