I see the same issue and have submitted a ticket. I find that when I use a preset that has a preset variax model (i.e. guitar model) forced, all other presets lose the "Don't force" option for the preset variax model. This makes all other presets select a guitar model and ignore the current setting on the variax itself (i.e. the select knob). I believe this is true for the Volume and Tone settings too... i.e. the "Don't Force" option is no longer present. I will verify that next time I sit down with the Helix.
If I disconnect the variax VDI cable, the "Don't force" option comes back for the presets. As soon as I re-connect the Variax, the option goes away. I also see that the Helix ignores Variax controls if I connect the Variax after powering up the Helix. If I power up with the Variax connected, the Helix responds to the Variax controls.
My current plan is to always have the Variax connected at power up of the Helix and configure every preset to use a specific guitar with forced volume, Tone, and tuning. Hopefully Line6 will fix the issues with "don't Force" options.