For anyone else coming across this in the future, I had this issue (flickering footswitch action, as the OP describes). I took the cover off, found the small gap in the plastic casing around the footswitch where you can see the spring and the switch's contact points, and hit that with DeoxIT, and worked the switch for a few seconds. Completely solved my problem. Much like mixing consoles, these things are surrounded by dust/debris them night after night on stage, and as well engineered as the Helix is, sometimes crud gets on the contact points. I went ahead and hit all the switches with DeoxIT while I had the cover off, just for good measure.
DISCLAIMER: I am a touring pro musician, NOT an electronics expert or an authorized repair technician for Line 6. I don't know what impact following my suggestion may have on your warranty, or if it will solve your issue. I just happen to be big on finding solutions I can apply on my own. Hope this might help someone down the road.