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The ePub could be an orphan?
If changes, even very minor, are made to the filenames calibre may loose track of the books. One cause is if the library is used from Linux and Windows, they treat upper/lower case in filenames different. Another cause is if you accidentally have changed the filename.
Copy the ePub and run the library maintenance to check your library.
You may have to manually add back books that calibre has lost track of.
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