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dwanthy is right, don't use multiple methods of sending your books to your reader. What ends up happening is that one will overwrite what the other did and you end up with neither of them working right.
Like others have mentioned I only use Calibre to send the books to my reader. Once they are on there though I will use the Sony software to manage the order of the books in my collections. I do that by opening the reader in the Sony software (with Calibre closed) and manipulating the books directly on the reader itself, not by pulling them and restoring them later.
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