Lol of course people read it, but sometimes those instructions don't work. I've updated my Helix several times and never had this issue. I found this old post which fixed it. Note button 12 and 6, not 1 and 6 as the post above this states.
- Quit HX Edit! Don't start it again until you're finished with everything following.
- Go here and download the Line 6 Updater (in case it's not installed on your machine already):
https://line6.com/software/
- Also download the "Flash Memory" from there (it's the actual update).
- Install the updater.
- Reboot the Helix while holding down switches 6 and 12 (this will take you to safe boot mode).
- Start the Line 6 Updater, select "Offline Mode" and see whether it finds your Helix.
- If yes, select it and choose "local file". Point it to the Flash Memory file you've downloaded.