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Windows was able to fix the issue. But now all the my document files are missing. Are there any free tools to attempt recovering them?

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Recuva is free software by the makers of ccleaner and defraggler (also awesome programs) I haven't used it myself, but i'd immagine it's good for what it tries to do.

Just bear in mind it's not always possible to recover everything :)

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I have had many failed attempts at recovering files when one of my old hd's was on the brink of dying, it restarted the pc and took absolutely ages. –  PrivateSniper Dec 17 '11 at 1:06
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This blog has a good amount of info on what Chkdsk does with the files on 7, and how to get at them, and I can't describe it any better myself, so... :)

chkdsk takes all the files it could not figure out where they were supposed to go and places them in a found.000 folder that is located on the root of your hard drive. However this is a hidden folder.

To view hidden folders you need to navigate to MainMenu -> Tools -> View -> Hidden files and folders fill in the bubble for "Show hidden files, folders, and drives". you also need to uncheck the box next to "Hide protected operating system files"

After this you will see a folder called found.000, open it Inside you will find many folders called dir0000.chk, where the 0000 is an ascending number. Each of these folders contain groups of files that were recovered.

found.000 folder

Keep in mind that there's a very good chance that not all of the files will have been recovered; and some of them may be there, but damaged.

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