I was able to get a working shadowmap. You have to import the model as FBX with two different UV sets. This is possible to do in Blender.

It's been a few months since I worked on it though, so bear that in mind. When you say sub-meshes, I think you are just referring to different closed sets of geometry? Or is it something more technical than that?

See my games here: https://www.indiedb.com/company/michael-klaus-schmidt