I was happily generating new meshes with the new trace tool (it's amazing), meshes for 4 skins were already done when suddenly after a 0.1s stutter/pause my project completely reset - attachments which were made into meshes went back to images, draw order of attachments got reset too. I restarted Spine which is when I noticed a new update was just released. I can only assume it's some kind of issue with the new launcher because otherwise everything works fine - no crashes or errors.
EDIT: Seems like a trace tool issue? Possibly related to skins, or changing the slider for trace tool's "Detail".
EDIT #2: Alt+tabbing out of the Spine app seems critical somehow. My whole project completely reset again after returning to the app.
EDIT #3: I can get my progress back if I quit the app without saving and reload the saved project file.
EDIT #4: Hasn't happened for a while now. I'm done with my meshes for now.