So, quick update.. I found out every time I get out of the chapter select menu, and go back in, my progress is gone. I don't know what's causing this, but I can't really progress through or play the game like this. I hope a solution is found soon, or if the file is just bugging out for whatever reason.
Sorry to hear you're having trouble with this, definitely the first time I've heard of this particular error happening, I know how frustrating it can be to lose your progress in a game. Lets see if we can get it fixed for you!
Are you playing using the itch.io app or just running the game where you unzipped it?
What operating system are you running? What version of it?
If you are in windows and not running as administrator, try right clicking on the game and picking run as administrator. See if that fixes things. It's possible this is a permissions issue stopping the game from writing the save files.
If that doesn't work could you follow these steps and then email me the resulting file at support at spookysquid dot com?
1. Find the directory with the game files.
2. Open config.txt in notepad.
3. add the following line to the bottom and safe the file: DEBUG_FLAG = 1
4. Run the game.
5. send me the file "errorLog.txt"
Hopefully we can get this sorted out for you so you can continue your game!