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One of the books on the device is "broken" and prevents all others from showing up. Or, more exactly: the FW is too picky and breaks, thus not showing all books. Search this forum for "books not showing up" or similar, you'll find many reports of the issue.
The solution is to delete all books from the device, and slowly putting them back in small batches until it breaks, so that you can ultimately determine which book causes the trouble. Usually, converting that book again in calibre (even from mobi to mobi) fixes the issue.
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