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Sigil has a plugin called ePub3-itizer that can convert epub2 epubs to epub3. I am positive Calibre can do exactly the same thing using an internal menu or command but they named it funny, something along the lines of "updating" or "upgrading" your epub. Best ask in the calibre forum and I am sure someone can point you to it.
As the author of Sigil's ePub3-itizer, I would be happy to summarize the conversion process steps if you have questions. Just ask.
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