Hey i just bought an HX effects, and ran into the same issue.
the exp would work up until changing a preset. Then obce you go back to any preset that has the expression pedal mapped, stops reading it as an input. I read everything there was to read on the topic and tried everything i read.
To those using stereo cables for your expression pedals. Line 6 changed their protocol to be able to read mono input as mono cables are more widely available. I solved everything just by using a spare mono cable instead of stereo cables traditionaly used in expression pedals.
let me know if anyone had success in a simular way. I bet there are more people out there struggling with the same issue.