Animals with name tags and animals within 20x20 fenced in areas are despawning. Note animals with name tags is very rare only happened twice in a time frame of 30 to 35 hours of game play. But fill a pen up with cows and start breeding them a lot and you unload and reload the area you will start seeing them dwindle down in numbers. I don't think this is affecting pets. Dogs, Cats, Horses, Llamas, and parrots. I have not seen them despawn at all yet.