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Gianni, I'm not sure I fully understand your situation. Calibre is not the one responsible for defining epub as a zipped collection of files. It is just working with what epub is. If any other program has accessed those epubs then that is just as likely to be responsible for any corruption introduced (assuming the file was not corrupt when downloaded) as Calibre.
Your OP said: "I made a backup of my library and, to my amazement, Caliber has not copied a large number of books giving me this error: ValueError: Not a ZIP file." You may need to explain that: how exactly you made the backup, and how any resulting problems are thought to originate with Calibre.
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