Are all your books on the SD card? What happens if you boot without the card? And then insert it?
I do have an external card in my Aura H2O with a few books on it. But most are on the internal storage. After a restart, I think there is a second flash of the home screen that might be when the books on the SD card are checked. I don't watch it closely enough to be sure. What you are seeing sort of sounds like this, but, the refresh to the home screen doesn't happen. Anything you do that does trigger an update does end up displaying all the books.
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