Yes, this is going to be an issue for now any time you encounter a crash. Crashing does not save anything on exit.
Right now we save the airport you were closest to when you shut down X-Plane normally, and restore that if you choose Resume Flight. Eventually we would like to restore you to the .sit file from the moment you quit last time, but it is not currently possible to do this with third party aircraft so this is not implemented at all.
In addition, if you were within the lat/lon bounds of the airport (or very near to it), we'll also restore you to the ramp or runway that you were closest to at the time of shut down. (If you weren't very near the airport bounds, we'll just re-initialize you to whatever runway/ramp start your prefs dictate.)