I don't know. Something sounds missing. I think either a sysex push of your file needs to be done, or otherwise there may be an editing application that is responsible for pushing such configurations.
I think you're forgetting something that you've done in the past. But, I'd be concerned as to why the BCF2000 lost all it's configurations. Either that or you do need to re-configure your show file with the current MIDI configurations.
Check your BCF2000 first to ensure your settings are what they are supposed to be.