Hello Joe,
[Topic moved here.]
When auto-detecting a stop, if you select the option on the auto-detection screen for MIDI output and the appropriate MIDI OUT port then to change the MIDI stop's state Hauptwerk will subsequently send the same type/value of MIDI message values for it that it heard from the stop. For example, if the MIDI stop sent MIDI note-on/offs with MIDI note number 63 on channel MIDI 5, then to control the MIDI stop's state Hauptwerk would send MIDI note-on/offs with MIDI note number 63 on channel MIDI 5.
If your MIDI stop instead needs to receive different MIDI messages (e.g. a different MIDI note number, or different channel, or different event type) from those it sends then Hauptwerk won't be able to configure it automatically (since it can't know what it needs to receive), so you'd instead need to configure the MIDI messages appropriately by hand, by right-clicking on the virtual stop and selecting the appropriate MIDI parameters manually.