If i remember correctly the game engine stores some files outside of main game directory (like save games). I will give you more details once Im back home.
No xD I simply forgot, sorry xD Short attention span.
Here you go:
Game Saves & Persistent Data Locations:
- On Windows, RenPy game save files and persistent data are usually stored in:
C:\Users\YourUsername\AppData\Roaming\RenPyGameName- The
persistentfile can also exist inside your game directory undergame/saves.