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Kobo's support told me that you have to eject the reader, and not just unplug the USB, otherwise you could damage the reader.
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They're saying this just to cover their ass. By default write-caching is disabled on USB devices in Windows unless you explicitly change it. You can verify this by opening up Device Manager, going to the properties of the plugged-in Kobo and looking at the 'Policies' tab.
I can see unplugging the Kobo in the middle of copying causing problems (maybe), but if you wait for the windows explorer copy dialogue to finish, or wait for the Calibre job icon to finish spinning, you'll be fine.