I could try running the Helix into my MOTU Micro Express MIDI/USB interface instead of daisy chaining MIDI. It has 4x MIDI inputs and 6x MIDI outputs, so I could send MIDI commands from Helix to the other pedals in parallel instead of series (no THRU needed). The question is, would this really work? What have I forgotten?

Sorry, I just saw your post.  This might work.  Does each MIDI input and output pair show up as an individual MIDI device or not?  If not, both H9s might be receiving the messages intended for the other H9 which would cause problems.  One might receive a message intended for the other from H9 Control and return an error to H9 Control for instance.