This is the second time in a few weeks this has happened to me in my world. I have a temple with a nether portal at the top and underneath are cells for villagers a set up for a trading hall I was building. It had about 18 villagers at the time of the first issue. I'm not sure whether it is in the spawn chunks but certainly is within a couple hundred blocks of world spawn. Working on a project several thousand blocks away from spawn i noticed two villagers from a city I was building had disappeared. Not really thinking it may have been more than a zombie, I made my way back to the temple through the nether and found all the villagers in the hall, the iron golems, the cat the dog and the hopper minecart from the drowned farm I built from a zombie spawner had all vanished.
Given that amount of work involved in capturing and curing all these villagers and setting up required trades this is a massive disappointment. Bad enough after a few weeks not having the heart to play from that disappointment this week I've been back curing and once again bringing in fresh villagers. Last night the last thing I did was cure a librarian and spent more than half an hour re rolling trades to get something I wanted. I logged out of the game afterwards just outside the entrance. On opening the world again today once again I've found every single villager, and the hopper minecart have once again summarily vanish and disappear on me. It is a futile exercise for me now. Why bother repairing the damage if it's going to happen again. The game is so laggy and so buggy at times it isn't worth the headache of playing since the enjoyment is being crushed by the amount of issues going on.
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I’m having the same issues. All of my named sheep, cows, and fish just disappeared. I’m also losing the carts on my automated rail (that’s been going on for quite a while now) and my armor stand disappeared.
I too have been spending a lot of time in the Nether, and a quick Google search produces lots of users reporting experiencing the same issue and questioning whether their recent time in the Nether is related. Others think their despawning occurs when the game crashes or when they or the mobs cross chunks. I’ve had crashes and I have crossed chunks (not sure about my mobs though), but I didn’t know to check my mobs after, so I don’t know.
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Just went and played again. Re-caught my fish then went to both of my nametag chests and all of my name tags except for the one in the item frame “label” have deswpawned. Different chests. Chests still there. So maybe the issue is that the tags are despawning and taking the mobs with them?
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The exact same thing has just happened to me, also for the second time. The only villagers that have stuck around are ones I’m honestly not bothered about.