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Somehow the underlyIng ebook files seem to have been removed from your Calibre library even though the database entry is still there. It is still not clear from your description how that might have happened.
If you have the books on your device, you could connect it, and then click on the Device view to get e list of books on the reader and right-click the book and use the Copy to Library option to get a copy of the file back into your library.
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