The problem is not cover modification it is that the EPUB file does not have a cover, instead EPUB requires reading system to render the first "screenfull" of the book as the cover.
So in my OPF file I have lines:
<meta name="cover" content="my-cover-image"/>
<item href="OEBPS/cover.html" id="my-html-cover" media-type="application/xhtml+xml"/>
<item href="OEBPS/cover.jpg" id="my-cover-image" media-type="image/jpeg"/>
<itemref idref="my-html-cover" linear="no" />
<reference type="cover" title="Cover" href="cover.html"/>
Are those lines not good enough, or somehow non-standard? It seems like if I do an EPUB->EPUB convert calibre basically just replaces the "cover.html" with "titlepage.xhtml" and wraps the cover <img> tag in a <svg> tag.
With regards to the command lineoutput, I had gotten the two error messages, and I wasn't really sure what they meant. They result from not being able to render the cover?
Manifest item 'calibre_raster_cover.jpg' not found
Guide reference 'calibre_raster_cover.jpg' not found