The problem is that iBooks does something extraordinarily stupid when importing ebooks.
It unpacks the ebook into a directory -- which it then names with a *.epub extension.
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You can use the AppleScript wrapper here to turn those back into real ebooks:
https://www.mobileread.com/forums/showthread.php?t=55681
Afterwards you will be able to import them into calibre.
Note: The *.ibooks folders use Apple's custom format, so I have no idea what challenges you may face in turning them into a format that other applications (like calibre) can understand.
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tl;dr
iBooks is a really bad piece of software.