I've had similar issues over the past few months. I rewired my entire pedal board, made sure all guitar electronics and outboard cables were good, fresh batteries, etc....and I was still having intermittent weirdness. I actually had complete signal loss right as I was about to rip into my solo during Estimated at the Grateful Garcia Gathering
Signal returned after a short time, but I had no idea what caused it to cut or return...not cool. Finished the set without any further issues, but man that kind of shit drives me crazy.
I finally (last week) narrowed it down to my Qtron Plus going flaky in a very strange and random way. I eventually just wiggled the mode knob on the pedal and could manipulate the signal loss. The sweep switch was also acting funky.
Not sure if this will help you as there are so many variables as JB mentioned, but ya gotta check and isolate all points in the signal path that could be causing the issue.