Logging off and logging back in should fix the issues preventing file deletion. And not much else is really outside the A Dark Place folder other than the passcode application from the documents folder. Deleting the A Dark Place folder entirely should clear everything up as well except for save-files which are stored differently. Deleting the save-file can be done by opening the game to the in-game main menu screen and pressing the Q key should then bring up a prompt asking to confirm a save-file reset. Afterwards, you should be good to go.