The FoC Game Cleaner application is now available on ModDB.
This (much awaited) application allows players to sync up their games to allow play between disc and Steam games. The application also allows users to remove any modified game content that will break online compatibility.
It was developed by myself and will continue to be maintained, as necessary. It will continue to serve as an interim solution until an official patch is released by Petroglyph.
Enjoy!
KH