Yes, you can load a flight with the aircraft in question and make changes. I generally do it while parked.
In Settinngs>Controls>Assignments you can create a key press to 'Reload User Aircraft'. I use (Ctrl+Shift+R). This will reload the aircraft, with the new .cfg settings. Make sure you save the .cfg changes before reloading the aircraft.
You can do the same with panel.cfg changes.
Dave
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