I can see a potential problem here. So H9 Control can save the connection by remembering the MIDI ports’ names. Therefore, if you have 2 identical MIDI port names for 2 pedals, H9 Control could mess them up. Did you set two different MIDI port names for your pedals?

Both pedals are using the same midiport as seen from the iPad. The routing is done inside the iCM4+. I don’t think that this could be otherwise: there’s only one port selectable in H9Control. Could this be related to incorrect device ID’s? I didn’t find an option to change these.