My girlfriend had exactly the same problem but she had to start the game again from scratch.
Where are the save files located? I may have encountered a bug, Im not entirely sure because its to do with a puzzle (the hunter card one - the cards that I believe I need disappeared without counting towards the goal) but Id like to start from the beginning again by deleting the save file since there appears to be no option for that in game. I have the DRM free version.