Corruption & saves wiped

I was playing and my PC suddenly crashed (some sort of system error, but not sure why it happened or what caused it, PC shortly restarted later). I lost all my progress and couldn't get anything back from the Steam cloud, or in any other way.
I still have the total playtime and achievements on Steam though and Steam says I still got the Retro pre-order skins. 
What I find weird is that everything seems to have got wiped instead of just the progress I made these last hours,