So this happened to me a couple of weeks ago after sleeping, when the game should normally save.
Oh no, my progress towards 500 days is doomed! I knew I had plenty of hard drive space, but no matter what I did, I could not make the game save my progress anymore. I submitted a report, but after a few days I decided to do more research. I found some posts, both here and on the Steam forums, but nothing consistent or specific, except that a few them mentioned Steam as the problem (although this message had also popped up on consoles).
So I checked the properties and decided to get rid of the cloud synch, since I only play on one machine anyways.
Success! My save file can save again, my progress has resumed.
I have no idea how this happened, why this worked, and if the problem will return, so if anyone has good info on this, please reply. Also, I wanted to get a potential solution out there in case this happens to anyone else. I mean, I can't be that special, can I? Maybe I should play lotto.