I had the same thing happened to me last night. I crashed my Munar lander full with experiment samples, and I intuitively pressed F9 to load my quicksave, only to find that I lost a few hours worth of science activities on the Mun and Minmus. However, before I exited KSP, I made a backup of the save folder right away before KSP create any new autosave. It is my understanding that during exit, the game will do an autosave. After I exit KSP, I renamed the current save folder to something else (as a backup just in case this procedure doesn't work), and renamed my backup save folder to save folder. Voila! I got KSP back to the latest autosaved state. This will only work if no autosave happened after the botched mission.