I was checking out the save folders in factorio (while playing, stupid i know) and when i went to save I was presented with an error, after which factorio promptly closes. For some reason after this happens the folder that factorio tried to save to no longer exists (i'm assuming because it overwrites the folder?).
In the example I was trying to save NewGame, after the error/crash the folder NewGame is longer within the saves folder. Fortunately all i had to do was reload the latest autosave but figured I'd mention this.
Changed the behaviour (for 0.2.9), when the file saving encounters error like this (access denied and such), it will show the message but not close the application, so you can sort it out without losing the game state.