Originally Posted by JSWolf
You are going about this all wrong. To change the cover, you do not want to convert the ePub > ePub. That has the potential for making a right mess. Don't do it that way.
Go into the metadata editor and drag the new cover on top of the old cover and click OK. The use the Modify ePub plugin to replace the existing cover with the new cover and you will have your new cover without going ePub > ePub.