Joel,
I don’t have the answer, but I can say that any time I have shut down the house 12/24 volt system when I restore power many of the circuits are not as I left them. For example restoring power might lock and alarm the doors, turn on some lights, or do other things that make no sense. I would have to go through everything to restore things to the way they were or should be. After that everything is OK.
I know on my coach prior to shutting off power the Watchdog has to be taken off line in a specific procedure. Dump valves, pocket doors, bed lift are all things that need air pressure to operate correctly, and if the buttons are pushed prior to having air pressure their action is screwed up until pressure is available and you play with the switch.
The generator fan is run when the generator is producing power I think. It has nothing to do with the AB switching.
But shutting down the coach 12/24 volt system should have no impact whatsoever on the AB system or anything you describe. I do know however if the house systems are shut down it disabled the Prevost so I couldn’t start it so there is some relationship between the two, but I thought that was just the alarm system powered through the house that kills the start circuit for the bus.
When I replaced my 50DN I did what you did and shut off the coach 12/24 and when I was done all I did was turn them back on and it was like nothing happened.