in reply to Deleting corrupted perl files - modifying the perl runtime

Why don't you use find (1) or File::Find to find all your Perl files, feed them into perl one by one using the '-c' option to see if they compile, and make a list of all of those which don't? You can limit the search to folders where these corrupted files are, and can vet that list manually before condemning them to the bitbucket.