...OK, there's a v2.0.1 up now which fixes a minor case sensitivity issue (...\CFG\file.name was not being recognised as being the same as ...\Cfg\file.name when determining mod file changes).
I also tightened up the folder renaming feature (there was nothing wrong with it - I just made it more "Windows Explorer" like in behaviour).
Just install over the top of the current version.
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