I'm experiencing similar issues with my Helix now after many months of no issues.
I've used it for a few gigs, after the 2.0 update without issues.
The past few days I am getting constant intermittent freezes. In the PC Editior, or editing patches. It seems to be triggered mostly by editing and occasionally the controller will just freeze up. The only change is I started using the Helix in the effects loop of my Mesa. Before I was using the AMP and CAB sims.
Very frustrating. Yes I have tried backing up my patches, re-flashing, re-setting and re-loading. I have tried modifying and re-saving my patches too. Not having any joy.
Anyone else in the same boat?