Many of the Synplant 2 patches say they're running in compatibility mode and ask me to update them, but when I click update, reloading the patch still shows the same dialog warning. Updates to the patches either aren't happening or are somehow reverting back.
Anyone know how to fix this?

Just "save patch" (assuming you like the upgraded patch) and Synplant will save the preset in your user folder. Essentially the "upgrade patch" is really an "audition Synplant 2 version". Which I prefer TBH. Hope this helps.