When you edit the .FLT, under [Sim.0], there is a field where you can set the tail number, but it doesn't have any effect. When you load the flight, the plane uses the last tail number set by the user in the worldmap. This means you can't set a specific tail number for your mission, and the tail number that is used may not make sense (e.g. wrong country, invalid number).
This bug has been present for over a year. Of course it doesn't have a high priority, just wanted to bring it to your attention.