I have also lost all my variax tunings in my Helix LT (with JTV 89F) with the 3.71 upgrade.
In HX edit sofware, all presets show "Don't force" for Model and Tuning, all strings are set to 0.
BUT I just clicked on Per Preset Instead of Global, evrethinhg looked OK
Then I turned off and on, a rebilt has been done and it sounds like before. Yeah!