You shouldn't need to reload the organ in Hauptwerk - changing the MIDI assignments on the settings screens should take effect immediately (provided you use Hauptwerk version 1.20+).
I'm afraid I don't know the controller number, but I'd try channels 1, 2 and 3 and each of the common controller numbers listed in the Hauptwerk help file if you haven't already (1, 4, 6 and 7).
Martin.