If your source is an ePub, there is no need to convert ePub > ePub at all.
Once you have the DRM stripped, you can edit the XML file that displays the cover and you can replace the generic cover image with a proper cover. Once done, you'll have a cover and the ePub will still be as it was (except for a proper cover).
Converting to HTML or RTF is asking for trouble. If you do not start with ePub, it's not going to be so easy. If you have a Kindle, still start with ePub as when you have the proper cover in the ePub, converting to Mobipocket is easy to do.
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