I'm on my first playthrough, but I can access second playthrough stuff like the Abyss and the Skit Viewer. I've beaten the game before, but this is a different file. Is my game disc messed up?
You just answered your own question. It doesn't matter what playthrough you're on, so long as you have System Data that recognizes that you've beaten the game before.
Once you've beaten the game, you have access to everything in every file. At least, you do so long as your System Data is intact. --- State Alchemists do what they're told. Like kick butt. Fascism: You have two cows. Your government takes both and shoots you.