Note that an ePub is a zip file, so if you convert from MOBI to ePub you can unzip the result and edit it as needed. Also, it sounds like all you will need to do is edit the .opf and .ncx files. If you are using Calibre to go back to MOBI, you may even be able to leave the skipped HTML files in place because Calibre will likely prune them.
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