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If you do it in Calibre you need one master xhtml file which only has a TOC with hyperlinks to all the chapter xhtml files. You then add this one master file and Calibre will bundle all the files into a single zip which can be converted to ePub.
If you're the author/publisher you may just want to use Sigil to combine all these xhtml files into a single ePub instead. Using Sigil won't flatten/rewrite your existing css styles.
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