I don't really understand much about effects architecture. Coming at your issue from a different angle, what happens if you "lock" your keyboard tones (including Upper 1) before selecting the registration with the MIDI file? This should prevent the tone itself from changing; not sure about its related MFX.

The BK-9 has a pretty straightforward set of menus that determine which channels are output via MIDI, whether or not the output includes SysEx or just note-on, etc. If you scroll through the menus with the manual handy, you might be able to figure how to send the desired output to your DAW. My $.02.