Combining Skinned Meshes no animation

I've been combining skinned meshes and have been able to succesfully combine them and remap the bones and weights etc. If I combine them using references directly from the model prefab they animate fine, however if I seperate each skinned mesh from the character prefabs (e.g. t-shirts, shoes etc) and then reference those the character no longer animates?

I'm unsure as to how I can load these from the resources without losing the data, the alternative seems to be having every possible combination of clothing on the mesh and then linking those up to my mesh creation manager.

Ideally I would like a instanced manager within the scene and then seperate skinned meshes within the resources folder in organised files so I can just assign them from my mesh options and build at runtime resulting in 1 combined skinned mesh that animates.