Don,
Does you RV connect the alternator to the coach batteries with just a 12 V high current solenoid like in my Class C?
If so, you might want to measure the voltage on both the input and output side of the solenoid when the coach batteries are low and the engine is running. Obviously those voltages should be identical. If not, the solenoid contacts have turned resistive, which could explain why your RV battery bank isn't getting charged as it should be with several hours of driving.
I've had this happen twice in the 10 1/2 years we have had our Class C.