I am having the same type of issue (Helix LT) I changed the wah (exp1) bypass on a bunch of presets (most of them built from the same template) from bypassing with the toe switch to bypass the wah with 99% position, 1000 Msec, and Toe Down behavior. I save each of the presets with the change. Upon opening any preset that I haven't made the bypass change from the toe switch yet, going back to the any of presets that I've made the above change to, the behavior is reset from Toe Down to Toggle. This happens when I open unmodified presets regardless of whether I modify or save the preset . But if I then change the behavior on just one of the modified bypass presets back to Toe Down, even without saving, most of the presets I've modified change back to Toe Down. But some stay on Toggle. I can't figure out what causes some to change back to Toe Down, and why some stay on toggle.
I did a backup/reset/restore, with the EXP1 parameters as above, behavior toe down. After restore, all of the presets had the behavior reset to Toe Up (not toggle, and not toe down as they'd been saved)). Changing them back to toe down, save, and go to another preset, and SOMETIMES it is reset. But not always. I haven't been able to figure out any pattern to it. All I can say for sure it that the bypass behavior setting is not stable.
If I reset the exp bypass as above, and open a preset that doesn't have a wah or block that uses EXP1, there is no change to the behavior parameter. But if I create a preset with just one block of any type, and assign EXP 1 with the above parameters, the behavior parameter will change in multiple presets as I change it, regardless of saving.
If there is a test someone at Line 6 wants me to do, I'm game.