Having the exact same experience as OP. Nothing like spending $1500 on a piece of equipment, following all the instructions provided to update, and immediately corrupting it. And it's a Saturday so it seems line 6 customer service / tech support is not reachable.
Can't even get manual reset to work, or installing back to original version firmware.
Resolved this, had to try different computer usb ports. Several ports later, the helix booted in update mode. Everything worked as described. Loving the helix after the initial annoyance.
Here was the answer emailed by customer support:
First, please try holding down footswitches 6 and 12 (the two on the right next to the expression pedal) while turning on the unit. This will put the Helix into update mode. Once it's booted up, try installing the latest firmware from this state. If that doesn't work, please try the process again but instead boot up holding footswitches 9 and 10. You can also try swapping out USB cables and try all available ports. Sometimes just trying another computer can work as well. Make sure you also have the latest version of Line 6 Updater which can be found here.
