I have the same problem with the Helix app on Mac OSX. I will try your suggestions.
I'm running 10.11.4 and I had the problem with Helix app 1.04 and also still with the new beta 1.10 (which is very cool btw). I have an iMac and I started running it in a USB port directly in the iMac. The Line 6 updater works fine, no problems there. However, both versions of the Helix app display the "can not connect to device " message after a while. The connection appears to remain in place longer when connected through a USB hub strangely.
I also checked that in Preferences the audio input in/out is not through Helix and no other audio application is running. I hope this will be fixed soon, because I can't export "Setlist" let alone "Bundle" because the connection will be lost before the export is finished. It seems that it may be a problem of OSX though ...
