They will lose the pedal. I was wondering could this be related to inverted polarity of the pedal or a TRS plug... Well I am no expert. I tried also to keep the polarity setting normal. It did not make a difference.
EDIT: Also I noticed that when I unplug the external pedal, the integrated pedal switches to exp 2 and gives a normal response. When i plug the external back again, the Helix pedal switches back to exp 1, but the external doesn't give a response.