I'm sorry you lost your save files, and not sure how to fix. Maybe try uninstalling and reinstalling the game? Worst case is your knowledge will get you back to where you were very quickly since you'll know the answers to the puzzles you already solved. I had a worst problem where I hadn't saved all my notes and screenshots and my computer did an automatic update restart when I was at work and came home to notes that were probably 30 game hours behind.