Hey John:
It's going to vary from motor to motor, but on my eFlight 15, the shaft is plain with no set-screw flats or circlip grooves or anything. Given a shaft like that, all you should need to do is get a precision ground shaft in the right diameter (from someplace like McMaster-Carr), cut it off to length, and put it in the motor.
The two potential problems that I can see to that are that the motor manufacturer used a slightly over- or undersized shaft, or that you have a motor where they got fancy and used a circlip (in which case you need to sweet-talk a machinist into making you a shaft with a groove). I doubt that either is likely, and a flat is something that you could probably cope with.