Ok - it's all fixed now. When I reconnected the house batteries, everything worked like it never happened. I assume this means the generator starts off the chassis battery, and that the generator popped a relay or something when it turned over but didn't start. The relay was somehow reset when I disconnected/reconnected the house batteries, and when the chassis battery was charged.
Confusing how a dead chassis battery can have that effect across systems, but it's a good learning point for the future. Interesting how the auxiliary start switch was in place specifically to start the motor off the house batteries when the chassis battery is dead, but it didn't work this time.
Thanks to everyone for the suggestions!
