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It sounds as though you have a corrupt file system. Make sure that you ALWAYS use the "Safely Remove Hardware" tool before unplugging the USB cable.
I'd recommend that you use Windows Explorer to copy your books off the Gen3 (just copy the "eBooks" folder), then reformat the CyBook's disk (again using Windows Explorer), and copy the "eBooks" folder back again. This will do no harm to the Gen3.
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