I came across this thread via a search. I was having the same issue described here - sporadically, the sound cuts out when switching presets via HX Edit. Otherwise everything else appears to be working normally on the Stomp. There is just no sound coming out of either the headphone jack or main outs. Power cycling is the only thing that will resolve it. And yes I have the most recent version of HX Edit and HX Stomp firmware. The frustrating thing is that the issue seems completely random and intermittent. No particular preset or obvious sequence of actions triggers the loss of sound.
I contacted support and was told to factory reset and reload presets one-by-one in case it was a faulty preset. I opted not to go that route yet. Instead, I tried switching USB ports. I had been using one of the USB2 ports (tower computer with multiple USB ports on the MoBo). I moved to one of the USB3 (USB2 backwards compatible) ports a couple of weeks ago which seems to have helped. Hard to tell if the issue has truly been resolved, but so far the Stomp has run perfectly ever since... and much longer than I was able to before.
This has me thinking the issue may lie on the USB controller/driver side rather than with the Stomp. Just my $0.02 in case this helps anyone trying to troubleshoot the same issue.