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It sounds as if you are moving the book files yourself? You should not be doing this,
With iTunes you should use "Connect" from within Calibre and then select iTunes. Once you have done that you can use the Calibre "Send to Device" command to get the books transferred into iTunes for later transfer to the iPad. Doing it this way ensures metadata is set correctly, and also allows you to see from within Calibre what books are in iTunes.
With the Kindle you can also use the Send to Disk command from within Calibre to get books transferred across USB to the Kindle. Calibre also has support for sending books via email to the Kindle.
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