Please can you give me a working example? I assume you mean the MIDI side of Helix is bugged and that I'm better off using the AUX jack instead?

In H9 Control click on the Pedal button in the bottom menubar, go to MIDI Settings, and then go to 'Assign MIDI CC Messages to pedal functions'.  You'll want to assign the pedal functions 'Increment and load preset' and 'Decrement and load preset' to whatever MIDI CC messages the Helix is sending out.