My computer files are missing.?

Well, something happened to my computer. It blue screened on me. And when I booted it back up. All of my files and folders were missing. See now. I would've easily gotten over the fact if they were just missing. But the problem is, these folders still are there. And some programs are trying to access them but they cant. I don't know how to describe it other than that. For example, I have a game called Minecraft. And in the appdata folder there were files stored there. But everytime I try to update the game It crashes. But if I skip the update. All of my save files and such, are still there. Thanks for the help.