Discovered 2 things:

1. The files for the graphics themes don't have to be in the vfd file for CCP to recognize and use them. You can leave them "raw" in the appropriate folder and as long as they are named correctly it will work.
2. I knew it was something simple, and the simple thing was my dopiness. I reversed the destination and the target file order and that's why it wasn't working.

Thanks, sorry for the waste of time.