For every stock aircraft I have made flyable I make a folder called "Patch Backup." In that folder I put the main ini file for that aircraft with the proper cockpit, avionics, etc. entries to make it flyable in it. Plus whatever other file like loadout data or whatever. If for some reason it becomes unflyable, I check the main ini file. If it has been overwritten I replace it with the one from the folder.
If I patch or get a DLC, I take the whole aircraft folder out and save it somewhere else. Run the game then swap out the new un modded aircraft folder for my modded one. The patch readme tells you what is changed and usually it does mess with much stuff from the aircraft folder. if it does I just cross ref update the data and then I am good to go.
