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There's a new plugin for Calibre called Modify ePub. It is great. For instance, if all you wanted to do was take care of the cover issue that some people are having, you could just modify the cover and not have to do a full epub to epub conversion, which would save your edits.
If you have a problem with a feature in Calibre if you go to that forum and let them know, usually someone will come along and provide a fix for you.
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