Hello Lawrence,
Hauptwerk has native support for the MIDI implementations used in MIDI-capable Rodgers organs of which we're aware, so I'd expect (although can't absolutely guarantee, since it's conceivable that your model might have been made with a MIDI implementation that we aren't aware of) that you should be able to use its stops bi-directionally with Hauptwerk, but you wouldn't then be able to use Hauptwerk's combination system, since the two combination systems would 'fight over' the states of the stops.
If you haven't done so already, please also have a quick read through the 'Playing Hauptwerk live from a digital organ' section of the main Hauptwerk user guide (pages 179-180 in the current v4.2.1 version), which covers some important points to be aware of (such as the need to choose between either using the digital organ's stops, or Hauptwerk's combination system).
N.B. also that if using Hauptwerk in a MIDI sequencer then in order to use a digital organ's stops bi-directionally with Hauptwerk you would need to have MIDI going between the digital organ and Hauptwerk directly (not via the MIDI sequencer, and with the relevant MIDI ports disabled in the MIDI sequencer), since a MIDI sequencer won't understand the necessary Rodgers MIDI implementation, whereas Hauptwerk potentially will. Hence it's more fiddly to set up if you want to use a digital organ's stops bi-directionally with Hauptwerk and use a MIDI sequencer.