So the backend issue has caused saves to be destroyed and lost. We're so sorry about that, but for most people you will have to start from the beginning. To quickly get your progress back, selecting ESC and pressing "skip to [x] ending" will quickly allow you to get your progress back. Again, this will never happen again and we apologize for the inconvenience.
Also a note, uninstall and reinstalling the game will not remove your key. You will always have access to the game as long as you have a working Steam account once the key is claimed.