I'm having the same issue on an older iMac with the most current version of El Cap, and USB 2 ports.
I've tried 3 different cables - one with a "wart" with no success, and discovered when I wiped out my brand new Helix last month, that I need to resort to booting the iMac into Safe Mode - holding the Shift Key down on boot.
Even tonight, the Helix app would only export a bundle successfully in Safe Mode after I drag-and-dropped the presets I'd been working on safely into the Finder.
Before the drag-and-drop, I had to Force Quit the Helix app 4-5 times because it would start to export and get to 1% - 8% tops - and go offline, and then there's no way to quit the app. After the drag and drop, I had success exporting a bundle. Go figure.
After my presets and bundle were safely on the iMac, the update to Firmare 1.04.3 went fine in Safe Mode. As an extra precaution, I recommend downloading the Firmware Update from the Downloads page, and installing it using the Choose File button in Line 6 Updater. I don't trust the USB at this point.
I suspect El Cap as well, and hope to see a resolution soon. I expect better from Apple. This issue has been reported since December, if not sometime in November that I'm aware of. I know there was a post from Line 6 on the HD500 forum, that there were issues with El Cap. The local Line 6 techs have had Helix's returned that failed the update process and were wiped out. They have brought them back on a Windows computer - without the presets that were created.