can't you just have different control modes?
Yes, as AWwrgwy has said.
In mode 1(Aircraft)
My Toes brakes in aircraft are mapped to keys C & V (the default), I used to have them on the analog brake axis for the toes, but CH gear lets you change the toe axis to a key press instead.
In mode 2 (GV's)
My toes brakes are still programmed to C & V so I simply remapped the GV S(brake/reverse) and W(accelerate) to C and V instead.
The range dial was on C and V in GV's so I had to change that (remap AH Gunner) but thats all.
I like the brakes for the aircraft on the pedals don't think I will change that.
I haven't, I still have them on the pedals