The minor change refers to the book text itself. Not its layout, css, etc. If the text content has had major changes then indeed it must be a new book.
Changing a book from epub2 to epub3 does not mean major changes to the book text content. So adding a uuid when a perfectly good id already exists will not be part of ePub3-itizer.
I will look into adding such functionality to Sigil or providing a plugin at some point.
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