Thanks for your reply - it's good to know that I'm not the only one with this problem. I uninstalled Helix Application 2.01 and installed the 1.12 version again, and it works with the 1.12 version of the firmware. I guess I'll stay with that until they take care of this problem.
As you can see in my screenshot, I have the Firmware version 1.12, and I am getting this error while trying to update my Helix. I downloaded and installed the Helix Application v2.01, and my Line 6 updater was already v1.09, but it got reinstalled as well. The Line 6 updater was giving this error both before I updated the Helix Application and afterwards.