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When you add a book or drop one into Calibre, it sees is as a new book. It'll will ask you if you want to import a duplicate book, but it will add it. You can either delete the old entry, leaving the new one as the only version in Calibre, or you can bring it in by editing metadata. Next to the big box that says "Available Formats," there's an icon of a book with a plus on it. Click on that, navigate to your new html, and click open.
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