Current known fixes:
Uninstall/Reinstall
This goes without saying, essentially turn it off and turn it back on again
Restore Factory Presets
You can attempt to restore Helix Native to factory you will lose your presets but it has worked for some
Computer name changed
Your computer's name may have been changed or if you are on a new machine you may need to go into your line 6 account and deauthorize the old PC and authorize the new PC using Line 6 License Manager. After authorizing I suggest uninstalling and reinstalling native.
Leftover registry files from a previous installation (what worked for me)
When a program is uninstalled some files maybe leftover, it seems as though the Line 6 uninstaller doesn't do a great job of cleaning everything out. Download Revo Uninstaller (free version) once its installed use it to find any left over files from previous installations and delete them. After that reinstall Helix Native, you will get a pop up that says you are opening native for the first time and the error should be cleared.
Side note: Its unfortunate that it seems like this is a common issue and most of the time people lose their presets when solving it. Really hope Line 6 does some sort of update addressing this issue.