Direct file table manipulation

This is a topic I wanted to raise after dealing with a ridiculous file system error.
When XP booted up with my flash drive plugged in, it performed a chkdsk that promptly broke three of my files. It failed to update the file table so the entries were still there, but I couldn't delete them because nothing existed therein. I chkdsk'd again but it didn't find any errors, because after all it was responsible for them. Force-delete utilities were unable to solve the problem because, again, the file didn't actually exist. So does anybody know how to directly modify or regenerate the file table?
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