> updated romfiles in subfolders. But the scanner keeps ignoring them and says
> that these roms are missing :(

Put them in a different rompath and it should at least scan them (although it will complain about the multiple set/folder).
It doesn't scan the folder because it already detected a zipfile for that set (and zip files are prefered). Well...since you shouldn't have a zipfile+setfolder in a rompath, it's not really necessary to continue scanning the folder as well.
What it clrmamepro supports is that you can have a set spread over multiple rompaths (still this is rather a dumb storing method 8)) but you will see another complain about it.


Roman Scherzer