I should have specified I use one midi switch to toggle the H9s on and off, so even if I saved the effect off when I hit the toggle the effect would kick in and then change the tone.

Off the top of my head, maybe the Looper algorithm? It might not work but worth a try.

Set the MIDI mapping for "Toggle between active and bypass" instead of "Left Footswitch" because the Left Footswitch can trigger Recording