The way i got around it was to fit a pair of 5v 18650 UPS modules. One for servos and pixhawk and the other for communications and pixhawk
I needed this as i am running solar so draining the main battery is a real possibility. A pixhawk has 3 separate 5v rails and im running power in to the servo and usb rails so as long as one of them has power the pixhawk will stay online.
I have a sail as backup propulsion but you could add a small air propeller and backup battery.