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Although an ePUB is a zip file, it is a specially packed zipfile. So you have to repack it equally. There are tools to help you though.
In general I would advice to keep the tools for the purpose they are created. Scrivener might be a great writing tool, I have serious doubts about its ePUB export.
If you know more about the structure of ePUB, it is not that hard just to enter an additional title and copyright page and maintain the rest. It is just simple XHTML.
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