Thanks, Paul. I think there is an issue with a particular set of steps that causes Dorico to exhibit the issue. I will document it below using screenshots. However, in summary, if one starts with a blank project and not one of the templates, adding a single player with an instrument, then delete that single player and adding any subsequent adding of instruments or ensembles, Dorico will create additional instruments in HALion SE starting with the next MIDI channel. I'm sure that is by design, but is where the problems start.
See if the following can be reproduced on your end. I am attaching a ZIP file link with the screenshots for the steps.
Create a new project, adding a single Horn player to the project. Added some notes. Everything played back and looked normal.
The single Horn player is deleted using the "Delete Player and Part Layouts". This will cause Dorico to delete the Player and the Part in the Layout, but will not delete the HALion SE instrument.
Add the single Horn player back to the project. Dorico will add the Part in the Layout and will create a new HALion SE instrument for the Horn, starting with MIDI channel 2 and leaving MIDI channel 1 in place. That could very well be by design.
Thinking that I already have a Horn instrument in slot 1 in HALion SE, I delete the Horn instrument in slot 2, and re-assign the track in Play for the Horn from MIDI channel 2 to 1. Everything plays back as expected and things are good so far.
This is where the problems start. Adding an Ensemble, in this case Strings, will cause Dorico to add the Staves in the Layout, but will not create new instrument slots in HALion SE and will therefore not having anything to assign in the Stave Tracks on the Play tab. Any attempt to manually add them to HALion SE and assigning the MIDI channels in the Tracks will not result in Dorico playing any notes added to those string Staves. In fact, I have seen Dorico actually reset the HALion connection, including the MIDI channels I have set up manually.
Hopefully the above makes sense and can be reproduced. From it I gather that we best not mess with how Dorico sets up instruments in HALion SE, but I think there is a fundamental problem, as the above can easily cause issues down the road as a score is worked with.