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I’d suggest backing up a step. Presumable, these dragons predate modern aviation, and have been using their instincts to avoid collisions for millennia before humans started flying. They’ve now got an older right to the airways, and historically, it is as well established as your right to walk down the street.

So if you want to consider flight rights, paperwork, and insist they get licenses or fill out paperwork to travel, you have to consider the political system, and who’s in charge.

Are the dragons the poor underclass? If so, they might have lost their rights to the airways when the wealthier, more powerful humans developed flight. Under this system, they might need licenses for most or all flights, or only be allowed to fly over the their own homes, or only at certain altitudes. Keep in mind that if a dragon doesn’t fly extensively while young and developing muscles, those muscles will be weak, and restrict the dragon’s ability for its whole life. Imaging a healthy human who always used a wheelchair instead of walking until they were 18. They wouldn’t be able to walk without serious physical therapy, and would always have more difficulty than someone who has walked since infancy.

Is everyone equal? Perhaps look into restricted airspace for human use craft, which are far more likely to crash than the dragons. If dragons want to fly in these restricted corridors, they might need to show they can avoid collisions with the less flexible aircraft to get official permission, or it might be more like a kid learning to cross the road safely, where it is basically a judgment call, and learning the rules as to how to recognize a legal and/or safe crossing point. But airspace basically belongs to the dragons, not the humans.

Are the dragons in charge? Either no humans fly, or they are extremely limited, and only allowed to fly limited, undesirable routes where they aren’t in the way of the dragons. Maybe only at times when most dragons are asleep. Although if your dragons use human-made aircraft for long-distance flights, who knows what might happen.

How would human aviation have been affected? If they need to defer to dragons, they may use blimps and hot air balloons more than fixed wing, and aircraft speeds would be restricted. Also, if dragons rule the sky, maneuverability might be prized over speed and carrying capacity because if the dragons say no to anything likely to kill them, then big, fast airplanes that need a huge turning radius are less likely to be developed.