Hello Aah,
I can't think of any way that you could reliably query Hauptwerk's current registration from external software or via MIDI, I'm afraid. Hauptwerk intentionally doesn't re-send MIDI output for stops since it would normally add unnecessary MIDI traffic (and MIDI has low bandwidth), and since re-sending states could actually result in incorrect states for toggle-type MIDI implementations. Hauptwerk doesn't use the Windows clipboard for its registration.
However, as long as both Hauptwerk and your software start from all-off states (e.g. by ensuring that the user has clicked the 'Reset' button on Hauptwerk's 'Audio, MIDI and performance' large control panel), then the two systems should stay in synchronisation anyway, since Hauptwerk will send always MIDI appropriate output from a virtual stop whenever it actually changes state by the user clicking on it, or when changing its state from a combination.