Gave it go and risked it to see what the process might be... backing up the files first.
Removed the mod completely
Reinstalled the mod (moving it to the same position in the priority order - left window)
Overwrite will not immediately show as red, you have to either:
Right click overwrite and selected refresh
orÂ
Install another mod, I'd suggest something that doesn't write to overwrite as I'd imagine you'd then have two sets in there and would have to try and separate them.
After that I went to the overwrite folder (C:\ModManager\overwrite), copied the contents and pasted them back into the mod that generated them e.g. Â (C:\ModManager\mods\Fores New Idles in Skyrim - FNIS)
Thanks Salvador/flyingspatula for the feedback :)