Erika wrote

you can either unlink the meshes so they don't reference a missing skin

Thank you Erika! I think you've led us onto the right track for a solution. Can you help me with an issue? We are duplicating the skin and making sure to unlink the meshes. However, we are finding that not all meshes are unlinked in the new skin. Is this perhaps a bug?

edit:
I think the issue with some random linked meshes staying in the new skin may be due to unused attachments in the original skin. I'm working with my team to investigate further. I found your comment here that helped me clean it up, unfortunately it removes attachments we want because they have no keys. Still digging!

Just want to chime in to say that unlinking the mesh is definitely the way to go! We ran into some issues with existing rigs and linked mesh so those will be a little more painstaking but I believe the solution still stands. Writing up documentation for my tech an animation team so hopefully we've figured it out. Thanks so much for your help Erika! Ciao!

I have a follow up question as I'm trying to solve the same issue. We are able to separate the atlas for each skin no problem. Our issue is that the JSON/skel exports reference the linked mesh of our default skin. So it spits out an error or just don't work. Is there any solution for this problem?