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It depends on what you are using as the reading software on the iTouch.
If you are using iBooks, then if you have the latest release of Calibre, then it WILL see an iDevice. Support for this was added relatively recently, when iBooks was made available for iPhones/iTouch devices running iOS4.
If you are using any other software on the iTouch then you need to use whatever instructions are specified for that software for transferring books. In such a case there is no automated transfer direct from Calibre.
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