Were you still using SubmeshRenderers from the old runtime?

That's being phased out in favor of: https://github.com/pharan/spine-unity-docs/blob/master/SkeletonRenderSeparator.md
It does the same thing but handles material replacement and multi-texture setup much better. It's also more transparent about which GameObjects it uses to render.

If you already had a large number of them set up, you may be stuck using an older runtime. Otherwise, it should be easy to just move your existing objects over to the new system. There shouldn't be a need to setup the separator slots again. Just need to remove the old SubmeshRenderer GameObjects.