Interesting, I always had to reboot my Fire when I'd copy books over via USB. But I haven't done that in a couple months now.
It may differ if you're copying amazon-purchased books that you downloaded to your pc for usb transfer.
It also may have been an issue that was resolved in a later software update since the last time I did it. When I did my test above, I did not have to do anything for the book to show up, but I hadn't yet used the reading app so I figured that was why.
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