Are you meaning mesh files cannot have spaces in the names? or were you stumped by same mesh file names which accounts to the duplicate resources.
Well, this is good news for you as i have started this today and will be making a button basically saying "prepare my folder for skyline" and it will convert, rename everything uniquely, apply uber shader with normal maps and specular maps if found, edit mesh data for the referenced materials, rename skeleton files and anything else that will be needed to make sure that folder will not clash. You will also have the option to make it recursive to batch convert / unique all folders while you have a
cupper.
I would like to make it so your 1tb of assets can be converted very fast.
Remember though, this does not account for bad meshes that have multiple lods, bad normals etc..
We also have a couple other tools which will help when you get a mesh with a material error in the asset manager like you had the other day. We are thinking to simply drag a .material file onto a .mesh file in the manager to change the material inside the .mesh being referenced and there is also the duplicate resource finder for those missing or problematic times to help identify the cause of resource duplication and to possibly rectify it.
This is now my primary job until all you users are satisfied with importing your models.