just yesterday, i had a pedalboard in which "MIDI note transpose" and "amsynth" wouldn't remove - they're both stable.... and also "stereo routing", which is unstable. but after a re-boot, things are fine.
...it seems like part and parcel with my observation (made in another thread) that after some amount of editing in a complicated pedalboard, sometimes things get weird in the UI -- transparent plugins, ones that won't remove, MIDI CC assignments not being re-learnable.
it's super-hard to nail down a cause. "save often, and reboot as necessary" seems to get me out of most situations. ...and an occasional "hold down the left footswitch while rebooting", too.....
i think i might be guilty of thrashing pretty hard on the MOD, but i haven't been able to permanently turn it into a brick yet! ...and, once i get any given pedalboard to a stable state while building, the MOD has never yet choked in performance!
so: thanks again to all the devs and all you guys in the community!