Livestock sometimes vanish when areas are reloaded/unloaded. I have experienced this with sheep (dyed and undyed) in a 6x9 enclosure. These sheep are fed and sheared multiple times, and potentially bred as well.
We have additionally seen this with horses on the realms server. The horses are tied up with a lead and in two instances armored. When returning/reloading the area, the lead can be seen tied to the post with no horse attached to it. One instance during a server crash resulted in a ridden horse despawning.
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I have experienced similar instances on my realm as well. it is an aggravation which really downs the gameplay I enjoyed when time and effort spent on endeavors are for naught.
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I have given up on trying to keep passive animal farms all animals I have penned, bred and/or sheered have de-spawned. With the exception to the few I have inside buildings, at some point I am going to try and create indoor pens and see if that works. I also have issues with villagers de-spawning, my villagers cells in my Iron golem farm never have but all by villager carrot and potato farms the villagers regularly de-spawn.
I have had this happen twice. Once it was 4 cows and another time it was a Horse with a 4 block heigh jump wearing Daimond horse armour. This really needs to get fixed.