I got my Helix this morning and I started the update procedure and the exact same thing happened,, "Boot Failure. Entered Update Mode!" and Line 6 Updater showed nothing,, my Helix was not detected in the Updater,,, even though it WAS detected when I started the update procedure to v2.82.
I restarted the Helix and my PC several time to no avail.
This was really nerve wracking, I thought I bricked my Helix without hearing how it sounds.
The solution was change the USB port from the front of my PC to the back, and restart Line 6 Updater,, then it appeared and I continued the update normally.
The strange thing is I started the update from the front USB ports.. but they stopped working in the middle of the update WTF~!
The front USB ports working perfectly fine with everything I used them for up till now.
Line 6 should really stress the importance of using the back USB ports of the PC while updating,, or fix their Updater software which definitely broken in that regard.