I'll give this a try.
I think the overall problem was you lost 1/2 your 50 amp shore power. In particular the half that was powering the converter, some of the outlets, probably one of the roof A/C,s your fridge and such) but the two pole tied together breaker (either in the coach or at the shore pedestal) didn't fully trip. If won't look tripped but it is. Happen to me with the coach panel breaker. When you turned off shore power while working with the dealer you reset the breaker and full power was restored.
For your questions -
If the battery disconnect switch was on then wouldnโt all of the lights in the coach be off? Or does the shore power override the switch? - If 115VAC is available to the converter it will provide house DC power needs even if the batteries are disconnected. Shore power does not override the switch but the indicator only shows that 12VDC house power is available but not what is producing the power.
Best practice with the battery disconnects is to only use them when shore power is not available and when you are not using the coach. IE when you are storing the coach. Think of "store" as cold, dark and quiet storage. Also ensure the inverter is completely shut down when you are not using the coach. Inverters can sometimes be wired directly to the battery and will still be connected ever when the disconnect is active.
Maybe the floor fan drained the coach batteries over two weeks? - Maybe, if the fan was plugged into a circuit that is powered by an inverter and you lost shore power.
Why was the chassis battery dead? - When the house battery disconnect is active (battery disconnected) the converter cannot provide a maintenance charge to either battery bank as the disconnect is between the converter and both battery banks. With a Hurricane or Windsport coach the chassis batteries are kept charged by the converter thru the house disconnect solenoid then thru the aux power (emergency start switch) solenoid then thru the chassis disconnect solenoid. Disable any of the three and you lose chassis charging via the converter.
Not sure what consumed the chassis battery. There are a few devices that are powered from the chassis battery but normally not enough to deplete the battery in two weeks. If it's the original battery then it might need to be replaced. You never know how well it was treated while on the dealer's lot waiting to get sold. Same for the house side. Run either down too deep to many times and they just can't hold a charge for very long afterwards.
There is a battery isolation manager that is supposed to prevent draining the coach battery, right? - With the newer rigs I'm not sure. My older Hurricane the Battery Control Center (AKA BCC) will open the aux power solenoid to prevent the house from draining the chassis or the reverse but it won't prevent a house item from draining the house battery or the same for the chassis. Leave the lights on (house ceiling lights or chassis head lights for example) and I'll still have a dead battery if the converter is off line or disconnected.
Not sure if the problem with the generator stopping is related or not - Not likely. A good probability for a 36 code is fuel related as the code indicates an "uncommand shut down". The usual suspect is the fuel pump overheating but you'll also get the code for low fuel tank level (under 1/4 tank) forcing a generator shut down so you don't run the coach out of gasoline.
2006 Hurricane 31D built on a 2006 Ford F53