Panda - when you open up calibre, by default it shows the books you have in your library folder, not what is on your reader. If you look near the top of the GUI, there is an area that will have an icon for "library" and if your reader is connected an icon for the "reader" and any "cards". If you want to see the books on your card or reader's internal memory, then you select the appropriate icon and then make you changes to deleting books. If you delete books from the calibre library, then those books are deleted from the calibre library folder on your computer. Thus, most of us add books to calibre and then dump them in a spare folder to avoid the chance of accidentally deleting them.
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