I had a very similar issue. Windows 7 machine. Upgrading my brand new Helix to 2.30.
Had to plug it into a USB port on the back of the computer. Essentially, a USB port soldered on to the motherboard of the PC. With Line 6 updater, "choose file" option would leave this thing in boot failure. So I had the Line 6 Updater download the data.
Once it was successful. The update automatically restarted the Helix, and then the Helix ran through a process where it seemed to go through every factory preset.
My takeaway? Updating firmware is not for the faint of heart.