No, it's purely a question of how many files there are.
Everything was working fine, until we added to our project images folder a folder called 'Players', which contained several thousand rendered frames of animation.
The next time we tried to edit a Spine project, all its images were missing. Not only that, but the 'TitleScreen' folder where the images were stored was no longer listed under the 'Images' tab in Spine.
We prodded and poked for a bit and discovered that every folder and file in the root of 'images' that came after "Players" alphabetically would not appear in Spine. Clearly, some arbitrary image limit was being exceeded while Spine was parsing the Players folder.
I moved the 'Players' folder out of the images folder and presto! All our spine projects worked again. It's a nasty hack though because (for various complicated reasons I'm not going to bore you with) our Spine and other images do need to share the same hierarchy, so it only "works" because "Players" comes alphabetically after "Images", and we can't use any images out of "Players" in our spine animations for fear they'll suddenly pop past the limit and disappear.