You should add this setting to your pbsv.cfg and it will automatically update any bans you make on your server by adding them to the servers pbbans.dat file.
pb_sv_AutoUpdBan 1
// [0=no, 1=yes] Set to 1 (defaults to 0) if you want PB to automatically update the permanent ban file (pbbans.dat) after each change to the banlist in memory.