> But I chose Yes To All but none were renamed/deleted/anything! Am I missing
> something?

Yes ;)
The renaming fails if the "new name" already exists. The sets+name check is fuzzy...it takes the best fit name which doesn't have to be correct though. To prevent overwriting an already existing set, the rename fails. You can use Scanner->Advanced->Move Not Renamed Sets To Backup instead. An enabled fixmissing will find possible missing files there then....after the namefix moved it there.

Roman Scherzer
ClrMamePro