Well, first of all if you only want to keep some US clones, you need to switch to unmerged sets.
Reason: If you don't keep parent files you skip the full-merged method where all files are merged into the parent set and -in case of split merging- you won't have the needed parent files available.
Renaming operations from one MAME version to another is one of the reasons why limiting the set list for auditing is a bad idea. If the set was renamed (and the new name isn't enabled), the scanner won't pick it up for renaming (hmm...actually I need to test this...but I'm afraid the renaming works only on the enabled sets). And hitting 'available sets' will only quickly check for the filename....and won't enable it since a new name is required.
What you can do is: Use the setinformation's window "select sets" option which allows selection with wildcards....e.g. %d=*(US)* to enable all sets which got "(US)" in the description string which is usually an indicator for US sets.....however, this is not limited to the sets you got.
The better idea is to not limit your sets....and hide completely missing ones afterwards.
See also:
http://www.emulab.it/forum/index.php?topic=22.msg439#msg439 on limiting sets...