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I never tried to convert a malformed epub with calibre myself. I am only guessing that it can repair some sorts of errors, and cannot some others. Having this said, here is how to convert from epub to epub.
- select the epub in calibre
- press "Convert books" in the top menu
- a new window opens; on the top on the right hand side you can choose the output format, choose "EPUB"
- press the "OK" button at the bottom
- wait until the conversion is finished
If this conversion does not help, you could upload the book here. There are some knowledgable people who might help you. If the book is copyrighted, you might at least show the report of the validator. It is possible that some people can help you based on this report.
At a second thought: Since your problem is not directly related to the kobo reader, you might consider consulting the General Discussions forum.
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