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I'm not sure about copying them directly from Sony Reader Library, but you should be able to add them directly from your device, which calibre should detect soon after you plug it in to your computer.
Be aware that the Sony software can clash with calibre, so don't have them both open at the same time, (I eventually uninstalled the Sony software after getting an Adobe ID assigned to my reader, and now I only use calibre).
With calibre open and your reader detected, (as shown at the bottom of the calibre window), you should be able to drag-and-drop the books from your reader onto calibre's library area and it will add them. Try it with a single book to make sure that it works and to get an idea of how long it will take.
(Presumably if you know where the Sony software stores the books then you could drag-drop from there instead.)
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