The starting batteries are not part of the coaches power pack , so changing just the two start batteries will have no effect on the house batteries because as soon as the engine is off they are separated.
Now if you were thinking of changing only two of the three house batteries , that's a different kettle of fish.
My two start batteries are 3 1/2 years old and the 4 golf cart 6 volts for the house are 6 , no problems.