Yeah, it was definitely some type of bug. The named/saddled and penned horses, penned animals, tamed and named dogs/cats, sniffers, as well as my Villagers/Prisoners in their small rooms that have all been traded with were gone. My zoo with enclosed "wild" animals however was unaffected. This world was survival only. No creative mode. Definitely frustrating.
It was two sessions. The first session I went mining but had got off. The next session was the next morning. I got back on and headed back to my base. I had not changed dimensions and my game hadn't crashed. I was also the only person who had played on the server for a few days. Thankfully I had a backup from before I left my base so I just loaded that up and had all my critters back. I haven't played since as I don't want to put hours in again just to have to load a backup again.