No worries mate! I had this problem before too, and nothing infuriated me more the having endless hours of game time played and earned ships and outfits go right out the window, so I feel your fustration. There is an update for Win EVN Override, that changes this and allows you to contiue your current pilot file. Sadly enough, I don't remember the link, I am truely sorry.
Would anyone else, perhaps, know the one I speak of?
Though I must warn you, I had several problems with the update, one being which that it made the game crash and become unplayabe unless I, ironicly, removed the added file labeled Update. Maybe someone could help with this too, no?