I ran into the same problem, after getting all my files out of Apples Books, and wanted to import them into Calibre. I did the following to fix it, in case anyone else runs into the same issue:
My solution was to use Archive Utility (Included with macOS - Just search for it using Spotlight). Open it, go to its Preferences and set "Use archive format" to "ZIP archive", so you'll get individual files instead of a single large one when compressing multiple files. Then just drag all your ePubs to the Archive Utility icon in the Dock, and it should ZIP all the ePubs individually. Then select all the newly ZIP files, right click on of them and select Rename in the contextual menu, and then just choose to replace ".zip" with ".epub", and select yes when the system wants to know if you are sure if you want to replace .zip with .epub.
Doing this allowed all my 600+ ePubs to be imported into Calibre with no issues, where two-thirds of them failed previously.
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