>>373892839
Well I've simplified this whoel thing to hopefully try to find where the issue is. I have a fully working project in unity, with a basic prefab linked to the original FBX. I open blender, import the original FBX in, do absolutely nothing, export with these settings to create a new FBX that's technically the same. Then I overwrite the original FBX with this new one, and the prefab no longer shows me anything but the bone spheres. None of the FBXs (neither original or new) have any shaders applied to them or anything. 

I've not mentioned the generic/humanoid rigging here because apparently that's not even needed if I didn't make any changes to the fbx armature, so can't be the issue?