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well...first of all...why do you keep the roms unzipped and want to check them unzipped to rezip them later? There is no need for it. clrmamepro works perfectly with zipfiles.
Anyway...don't forget, you got 2 official storing methods: rompath\setname\file 1 ... file n (for unzipped sets) rompath\setname.zip (for zipped sets)
The rest does cmpro for you. If you get a message like "the following rompaths don't contain any valid set", you probably store the set wrong (see above) or all are wrong named...then the name fix will fix that for you.
....or you can use the rebuilder to create "something valid" out of your mess.
Nothing happen to your files. Unneeded stuff is backup'ed by default, the rest gets fixed.
Anyway...I advice you to read the documentation and follow one of the tutorials.
 Roman Scherzer
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