Another thing. Seems that MIDI controller assignments don't survive my typical power cycling of instances, at least when on disk. Annoying to have to re-learn them all the time.
(I'm not actually certain what the repro steps are here. But these are steps I do, and it keeps failing. I would explore what exactly breaks it; it's something along these lines.)
1) Create a new instance, with an instrument plugin of your choice, and add a VST or AU FX plugin to the channel.
2) Create a new MIDI controller over there on the right of the screen, learn the controller assignment, and learn the plugin parameter to use for it.
3) Power off the instance, and save the server project.
4) Quit VEP, relaunch it and open the saved server project, open the instance and power it on.
=> MIDI controller will still have its source assignment but not its target asssignment into the FX plugin which will be blank and won't work.
I power the instances on only when I need them, as I have > 150 instances, one per instrument, as makes sense for Logic.