@IndieDoroid @[deleted]
I just had a similar issue, but it doesn't seem to be related specifically to Spine. Ever since updating to Unity 2020 (not sure if it happened on 2020.1.1f1 but its happening on 2020.1.2f1), I've been having issues where I have to "reimport" parts of my project. Just a minute ago my project randomly lost reference to one of my 3rd party Libraries (which are located inside my project, not in Packages or anything), and stopped showing a SkeletonAnimation in my Scene view. I only had 1 SkeletonAnimation in the scene, and was focusing on figuring out why the reference to my Networking Library was gone so I didn't test out too much with why the Spine animation disappeared.
I tried reloading the Scene, and I tried restarting Unity. Neither changed anything. I ended up right clicking on the folder that has my Networking Library assets, and clicking Reimport. Not only did that fix my reference to the Library, it made the SkeletonAnimation in my scene reappear.
The only thing that I can think of that might have linked those two issues: When I run my game, my networking library spawns the Player character by referencing my player-prefab in a Resources folder. All of my character prefabs are in the same Resources folder. When my project's reference to the Networking Library got screwed up and I tried to run the game, it tried to spawn the player and the error I got was essentially "Player prefab not found, try placing it in a Resources folder" (as though it didn't find the Player prefab, despite it definitely being in a Resources folder).
So, not sure exactly what is going on - but maybe you could just try right-click Reimport All on your project @IndieDoroid?
Update: Alright, I'm not sure if this is indeed related to Spine or not, but my artist just had the same issue. The artist was working on a scene, and restarted Unity and when he re-opened the scene, the Spine gameobjects were invisible. Doing a right-click Reimport on the prefab assets made them re-appear (maybe that does the same thing as the forced Update on the SkeletonAnimation?)
Info:
Unity 2020.1.2f1
Recent version of Spine runtime (from a couple days ago)
Artist is using a Mac
@IndieDoroid I doubt it has anything to do with it, but are you using Collab by any chance? Things are being screwy for us with Collab also.