rhino, there may be a setting somewhere that addresses it, but I am not aware of it.
So here is what I do when I encounter the issue: I open the epub using either Calibre's tweak epub feature or sigil. I then delete the "cover.html" text file. Then close the book back up and re-convert it in Calibre. The generic cover image should be automatically deleted from the book as it is no longer associated with a text file.
Two things to note: (1) The duplicate cover file is not always called "cover.html" so in those cases you have to look among the text files for the offending file. Often it is a file with "cvi" in its name. (2) Sometimes a "Cover" entry in the metadata TOC is still tied to the old/generic cover. If so, Calibre will delete the "Cover" entry in the TOC upon re-conversion because it is no longer associated with an existing file. If it does that -- and you want a "Cover" entry in your TOC -- then simply use Calibre's TOC editor to add a correct one in. It's really easy to use if you haven't yet tried it.
--Pat
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