Hhhhmmmm!
FTP is the way to go, retrieve from server ammend and send back to overwrite, or send new file of same name to overwrite. Why it gets over written?
You could maybe do a work around, create a new PB config file like PBtag.cfg then have:
pb_sv_load pbtag.cfg
In your server config, this will also prove you can upload file to your server via FTP, thus if you can't see this new file in your PB folder, then you have issues with your FTP.