If you're editing proper files (if manual), or using XGUI, all your config stuff is being stored in gmod/data/ulib_or_ulx.
We don't touch those if possible. (I can only remember once we ever did, wrote a automatic converter, and kept backups of the originals 'just in case')
If you're editing improper files, and our files on those locations specifically say 'do not edit this file', then, they may get overwritten.
(IE, don't edit files in /addons/ulib_or_ulx)