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Open the OPF file, in the top couple of lines look for version="2.0" change it to version="3.0" or "3.1" or whatever you need. Save your book. If you are starting from an EPUB 2.0 source file, then you will likely also need to run the Table of Contents tool to generate a nav file or create one by hand. Someday I might get around to making a button to automate those changes.
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