Unless the generator's connections to the coach battery were removed, the added chassis battery connection shouldn't affect the ability of the generator to start. The generator only needs 12V DC power from one or both coach batteries to start, if I'm not mistaken?
What year/model is your Roadtrek? Always useful info when troubleshooting. You can edit your profile under the User Control Panel, and add it in under "My RV", so it's always visible.
Check the cable connections on the coach battery. You might have to tug or wiggle them to make sure the cables aren't corroded inside the clamps. Repair/replace any suspect connections.
When the battery enable switch is in the "enable" position, is there power to the rear/coach lights, will the furnace fire up, will the TV and/or the Fantastic Fan work? If yes, then the coach battery DC power supply is functional and the battery has some state of usable charge. Hopefully enough to turn the generator over.
Does the generator try to start, splutter a few times, but then die? Sometimes you just have to be persistent and keep trying. Let it turn over for 10 seconds at a time, to get fuel to the Onan's carburetor, especially if it's been sitting for a long time. The fuel line from the gas tank to the generator may be dry or even partially plugged.
Is there enough gas in the vehicle's fuel tank? Must be well over 1/4 tank to feed the generator.
Is there enough oil in the generator? Won't run if not enough oil. There's a little threaded dipstick inside the casing. A removable panel allows access to it. Be careful not to break it off or drop it into the casing. They're very difficult to retrieve from inside the Onan's casing.
Try starting the vehicle's engine to supply a charge to the coach battery(ies) while trying to start the generator. It may help if the coach battery charge level is low.
Lastly, you might want to try Sea Foam in the fuel system as an additive, or I've had some luck adding fuel stabilizer to the fuel system to help de-gunk the carburetor.
If all else fails, maybe a service center can help.
http://power.cummins.com/onanpowerWeb/o ... ication.do