The ref should remain with the added stage and be lifted on the other when switched from cleanish to dirty. (as if the normal input is empty)
I made up several "keys" from 1/4" plugs for an amp I built. These "keys" had various opposing diode pairs and one with just a wire loop. The amp was a plexi with the one-wire and the lo inputs deleted.
One input was normal, one was the brite, and then when you plug into the brite and use a key in the normal input it went nutso fantastigain mostly from adding that second 1M from the jack on the normal.
See if that anecdote might give you some other ideas. You said you had a three switch relay in there, right?