It's weird. My above ground villagers and animals (because it seems to be happening to livestalk too) seem to be disappearing. However my underwater animals and villagers are just fine. I don't mean below sea level, I mean basically in reverse aquariums. My base is on a small island, so I dug out under it, put in glass and that is where my "fields" are.
Same with my villager breeder. Those have been just fine. I am not sure what the issue is.