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The Library app uses the database to display what is available and to launch the reader app for an ebook. That database only gets updated by a system program that runs from time to time. If you add or delete ebooks directly on the filesystem, the database won't instantaneously sync to those changes. There used to be a menu item in the System tab for starting that process directly, but I don't know if it is there in newer firmware versions. You can try rebooting the device and waiting a few minutes to get the process to update the database if the System menu item is not there.
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