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Are you using the Wireless or content server connections between CC and Calibre?
The wireless connection will automatically update metadata and can automatically update already loaded books they've been changed (if you've set preferences properly) but as far as I know there is no way to have CC automatically download new books from calibre.
Wireless requires you to select the books on calibre and press send to device, the content server connection requires you to browse for and select the books to download from the content server using CC.
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