Oh hot dogs.. you may have gotten really unlucky there if it was saving at the same time!
The game saves to this folder:
C:\Users\YourUserName\AppData\LocalLow\Trilum Studios\Cheeky Chooks
You can check there and see, but if on the main menu its showing up 'New Game' instead of 'Continue' it's because it cant find a save file. Check in that folder and see if its there, also that you are logged in as the same user.
When we launch on Steam we hope to get cloud saves working to solve this issue. I'm really sorry if you lost your progress, let me know how you go either way. I may be able to give you some kind of boost if you have lost stuff.