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It’s the iTunesMetadata.plist file that uniquely identifies a book. Once adding a book to iBooks on macos, that file was added to the book in the place where ibooks stores the book. On newer versions of macos, I’ve had to edit the metadata within iBooks to get that file to appear. I save it and add it to the original epub for safe keeping.
If you want to update the work, on macos you can unzip the changed epub into the proper ibooks folder. Some metadata changes I dont think will appear such as title, author, publisher etc. Those maybe can only be changed within ibooks. HTML changes work fine. Other changes in the OPF, NCX, and NAV won’t immediately appear since ibooks caches them during pagination. An ios update will clear that cache or you could delete ibooks, reinstall, and let the books redownload from icloud. All the time, I make changes to an ebook while keeping higlights and annotations.
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