I attached another scope to my rig and they both have Moonlite focusers. But one scope is much smaller than the other, and so the autofocus settings when switching between the two are totally different. When I switched the camera in the autofocus module it maintained the settings from the first camera. Am I missing something? Doesn't EKOS save the autofocus settings assigned to each camera separately?

I noticed the same thing. I think they're trying to fix that with the 'imaging train' idea that's in the forums.