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1st, is the book you are converting still DRM'd? Calibre won't convert DRM books (unless you have the plug-in for that).
2nd, what is the file extension of the book you are converting. If it is .azw (as I think most if not all purchased Amazon books are), Calibre converted it to a .mobi and that's what you moved to the kindle. However, you are probably still looking at the .azw file which wasn't altered. So now you've got two versions of the book on the kindle.
This later situation is what I've encountered.
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