So basically, I was playing for several hours, I got really far into the game, on a load screen my game crashed (not responding) and then when I reloaded my game I was pretty amazed that my quick saves and autosaves were all rolled back to a really early stage in the story.
After some more exploration I found that if you ALT + F4 after you quicksave/autosave it won't keep your save games, it actually deletes them and rolls them back to previous sames where you have quit the game from the menu rather than using other means.
Just thought I'd let people know not to ALT + F4 and perhaps quit the game from menu every hour or so, lest you have the same thing happen.