Apple does something weird with .epubs that you add to Apple Books. Here's how to recover them back after you import them.
Your books reside here, but they aren't actually epubs.
~/Library/Mobile\ Documents/iCloud\~com\~apple\~iBooks/DocumentsIt seems Apple unpacks them weirdly, so to export them as actual epubs, you need to do something like this [1] & [2]
# Copy the Apple version of the epub to somewhere
cp -r apple-epub-path.epub /tmp
# Enter the epub directory
cd /tmp/apple-epub-path.epub
# Generate an empty epub file
zip -X0 "$PWD/destination.epub" mimetype
# Add files to the empty epub file
zip -rDX9 "$PWD/destination.epub" * -x "*.DS_Store" -x mimetype[1] https://www.mobileread.com/forums/showthread.php?t=55681
[2] https://www.mobileread.com/forums/showpost.php?p=4304758&postcount=146