Hi,
Most RV's you can start the generator, and the normal system will connect the coach battery output to the engine starting battery. When My alternator went out, I was in Yellowstone, and started the generator right away. (belt broke, the alternator was actually fine). I turned on the charger, and drove to Flag Ranch, stayed a few days, drove into town for a new belt, was fixed in a short time by me.
I could have driven farther if needed, because the power steering was on another belt, and the water pump and cooling fan is served by both belts on my 97 F-53 Ford motorhome with a 460" engine.
Good to know that a small power failure will stop most of the things from running. The engine will not get a signal to run, the fuel pump will also stop. You where lucky to find a rest area.
Now I hope that you recharged all the batteries before starting the engine. It takes a lot of amperage to recharge the battery, and this can overheat the diodes inside, causing the new alternator to have a very short life.
If you have a inverter, my suggestion is to not run the battery low, and to use the generator to recharge the coach battery if you have been dry camping more than two nights. You probably have a 440 amp hour coach battery bank, and that can put a large load on the alternator. The cost to run the generator is insignifcant, and will take a lot of strain off the alternator and it's belt.
Another thing that the Cummins dealer probably already checked is for a loose conection. Disconnecting a alternator from it's battery is a sure way to melt the diodes inside it. This can happen if the alternator output wire is loose, and does not conduct power to the battery. I have also seen it happen to two people who have electronic battery isolator, where one of the connections melted, and the alternator output was not going to either of the batteries.
I would recommend if you have a electronic type battery isolator to install a mechanical solinoid isolator. Grainger.com has a relay made for forklift contactor, rated at 125 amps max, and has silver allow contacts. 6C017 if I recall right. Albuquerque has a Grainger branch, the Cummins dealer should be able to buy the part, they normally keep one on the shelf.
What I would do to correct the wiring is remove the electronic isolator, and wire the alternator output directly to the engine starting battery, then install the isolator to the coach battery with #4 or #2 wire. Turn on the isolator with a wire that is powered when the key is on or in ACC position, such as the +12 wire that turns on the radio while driving.
Fred.
Fred.