For sideloaded books on the device you can. Connect the device, go to the device list and select the books. Then right click on the and select the option to add the books to calibre (sorry, can't check exactly what the menu item is called). The sideloaded books should be added to calibre and you should get a message about any purchased and downloaded books being "virtual books". These do not get added by this method.
The metadata used will be whatever is in the book when it was put onto the device.
If you need to add the purchased books, you will need to Obok plugin that is part of the DRM tools.
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