If you're using Plex, then you can't use AniDB, unless you're using the 3rd party HAMA plug-in in which case you want Absolute numbering.
Instead,
convert your episodes to TheTVDB naming and then let Plex do it's thing:
viewtopic.php?t=2769

If must use AniDB, but don't want SxE numbers, then you'll need to adjust your custom format and avoid SxE bindings such as
{s} or
{s00e00}. The
{plex} binding is generally recommended, and that will result in HAMA compatible Absolute numbering for AniDB episode information.