In short, divide the career in two available “routes”. Let the user choose either the fixed or rotary route and make the various endorsements equally achievable in either. Also, make sure to generate appropriate missions for the chosen route.
It should also be possible to move between fixed and rotary, of course with the same requirements. If you take the rotary route beginning with a PPL-H and then want to fly some fixed wing missions you’d have to take a fixed wing PPL as well etc.