This is not a solution or a fix. This issue is a major gameplay issue that has been going on for over half a year now, and simply marking it as "Won't fix" is not acknowledging a major issue with the game.
I am having a similar issue on a realm, but my animals seems to be disappearing based on location. I have two separate areas on this realm, both of which are in different 2048x2048 maps, and they are a good bit away from each other; a 2048x2048 map or two in between them.
Location 1 is near the spawn of the map, as well as other people's areas on the realm. There have been no issues on animals despawning here.
I like to travel so I built up a new area, roughly 4,000 blocks south and 3,000 west of location 1. Here I found an amazing white horse, left it out in the fenced off stable outside, and one day it was gone, saddle, armor and everything. I then found two black horses and brought them back to this location 2. I bred them to about 7 black horses, and slowly they all disappeared to none. Somewhere in this, I also brought in two cows to attempt to breed them for meat and leather, and they disappeared. This seems to be happening whether I'm offline or doing something on the realm, and I have not entered the nether like the OP of this post.
So eventually I traveled again, about 1,500 blocks north and 500 to the east of this location 2. These two areas are on still the same 2048x2048 map. I did a similar thing to where I found 2 horses and bred them to about 8 horse. Now I am down to 4 as some have disappeared. These horses are housed in large area outside, with two sides being a fence, one side being a large wall with towers, and the fourth side is not fenced but it is a large ocean.
A solution to this issue would be much appreciated, as I have found 2 near perfect horses and both of them just disappeared with the gear and everything, it is extremely frustrating.
Thanks,
Nick
Mega spud, my despawning issue does not involve the nether, seems more based on which chunk I'm in. Definitely not crash related either.