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The HDD attached to my Pi with my ebook collection (with database files) is ext4 formatted and it works without problems. So in my opinion ext4 (alone) is not the problem.
Copying with CCC makes a 100% exact copy. But a copy from mac HFS+ to ext4 cannot be 100% exact.
Why not try just rsync without exact file permissions, you can set them on your Pi later (that's what I do).
Or copy using smb/samba. Also works ok from mac to pi (linux).
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