It is generally considered "wrong" to add highlights to a book, as they are not part of said book. They're commentary that you're making on the book, so they're separate. It's not even clear how you would merge the highlights with the book, as highlighting is part of the reading engine, not the book. You'd have to add a bunch of fancy CSS styles to draw shaded backgrounds around certain blocks of text to simulate highlights, I guess. Neither Kobo nor Amazon has mechanisms for doing that.
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