So, it looks like you (at some point) installed Part 3 over Part 1. When you do go to install Part 2 or 3, install them to new folders.
My suggestion:
- In the 0.41 folder (or in your personal folders - perhaps someone else can help you locate that, I actually play on Android), locate your save folder, and make a copy of it (just to be safe).
- Download Part 1 again, and install it in its own folder.
- Launch Part 1. Try your saves to see if they work. It's not impossible that the latest ones were corrupted, try older ones, and auto saves.
- If none of the saves work, you can try deleting the original saves folder and copying in the one you made in step 1 above. However, you may be out of luck.
- Delete the 0.41 folder version of the game - when you get to part 3, you'll probably want to install the latest version again.
NOTE: don't install any updates while playing parts 1 & 2; they are older versions, and haven't been updated. When done with Part 1, install the full part 2 version in its own folder. Once you install part 3, you can continue to update it until part 4 is released; then, the latest part 3 will be complete, and won't need updates either (do make sure to update it to that last version).
If this is too confusing, wait and see if someone can post better instructions. I'm fairly confident in my diagnosis of your problem, though.