Unfortunately, I couldn't figure out how to resume a saved flight (in the air).

I tried this by pausing FSX-SE, then saving the flight, but when I resumed the flight, I couldn't do anything with the switches/knobs (well at least not see the results of pressing a switch/knob), so that didn't help. To top it off, when I loaded the flight, it loaded my default panel state, so that leads to think that you might have to save the current flight's panel state as DEFAULT (making sure that Load Default Panel State is ON (or maybe the trick is to have it OFF? Hmm.)), so it loads when the flight is resumed. I'm not sure if this would include your current route though, of which it didn't reload after I resumed a flight like you did.