The locale.archive format stores MD5 hashes of locale data it contains, and the hashes are used by localedef to check whether a new piece is already stored in the archive - without checking for MD5 collisions.
I changed that upstream. Should be in the next rawhide build.
This bug appears to have been reported against 'rawhide' during the Fedora 11 development cycle. Changing version to '11'. More information and reason for this action is here: http://fedoraproject.org/wiki/BugZappers/HouseKeeping
Fixed in 2.9.90-20.