Playing Vanilla Minecraft on the latest snapshot (15w33c) on a LAN world with one other player. We found a village with a lot of villagers. At night, the villagers began going into houses like usual. I was in a forest away from the chunk containing the village. My brother died in the village and respawned away from it. When we returned to the village (still night time), all the villagers were gone. The houses were empty, not even zombie villagers. Zombies still walked up to the doors of the buildings as if villagers were inside, but there were no villagers.
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This sounds more like a legitimate zombie siege; yes, there should be zombie villagers after a siege, but they are then hostile mobs, witch can start despawning randomly if no player is within 32 blocks, and should despawn instantly if no player is within 128 blocks. If this were the invisible entity glitch, the villagers would still technically be there, so you would at least see doors opening and closing during day and hear villagers getting killed by zombies (if applicable) during night.
Dupe of MC-65040