I realized you could also update the Organelle OS to the new version:
This update allows you to change the global MIDI channel without messing with mother.pd. This way you can set the Organelle to receive on a different channel thant the fcb is sending, and everything should be fine. (sync is for all channels, so sync should still work).
If you do run the update, be sure to remove the old mother.pd patch in your Patches folder (if you put one in there)