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Just so it's clear -
If the epub doesn't have an iTuneMetadata.plist in its root, then iTunes will always generate one automatically on importing the file. In this process it scans the opf and extracts certain metadata elements as well as generating a couple of hashes and an ID number whose purposes are currently unclear.
If the epub does have a plist file in its root, then iTunes won't scan the opf metadata and won't generate the hashes or ID. It will simply use the plist as-is and ignore the metadata in the opf.
Any changes to metadata made in iTunes are written only to the plist file.
At the moment epubs do not appear to be included in the xml data created on exporting the iTunes library.
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