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Unfortunately, iBooks isn't available on Windows and Apple got rid of books in newer versions of iTunes.
If one downloads ebooks, say via Safari for iOS or Calibre Companion and imports it to iBooks, it seems initial book identification is based on checksum. I'm basing this on my experience with fanfics. Simple filename changes, it recognizes books that are already in library just fine and doesn't re-import. When there's a new chapter or edits, though, it imports as a new book even if identifier remains the same.
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