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Every book that calibre displays exists as a file somewhere on the device. That location may not be visible in whatever app you use on the device to list books, for example, a cache directory or a directory from some other, now unused app. Or the file may be in a format that your app cannot read.
The only way to check is to go over every book calibre lists and see where it comes from (you can do that by clicking ont he book and seeing the path in the book details area ont he right).
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