The autosave file (e.g., ~new.fy) only gets deleted when you exit the program. So if you change the name of the experiment on which you are working (e.g., Save As, or Open), the autosave file won't get deleted, and the next time that file is loaded, the program will prompt the user for recovery.
Another problem with autosave is that recovery does not happen unless the user selects File.Open. So if the user never saved the file, then the autosave file will do no good.