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Highly unlikely if the books originally came from Apple itself. If they are unprotected ePubs you copied into iBooks yourself you can copy them back into Calibre and do what you like with them. Assuming you're using a Mac and not an iOS device, drag and drop from iBooks to your Desktop then drag and drop from there into Calibre. Whether this is successful re the annotations depends on where Apple actually stores them. If embedded in the file it might work; if they're stored separately with some kind of pointer to them it probably won't.
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