What type of device do you have?
I'm using a Sony T1. When it's plugged into Calibre I see 3 new icons, Library, Device and Card A. The Library icon shows all the books in my library, and in the "On Device" Column, shows whether the book is on my reader or not. You can sort by On Device, by clicking the column heading. The Device icon shows which books are on my reader's main memory, and the Card A icon shows which are on my memory card. Depending on which view you look at will depend on whether you see the book or no on the reader. With the device and card views, if you then right click on the book, you can then add it to your library.
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