@BetterRed - you have a slightly unusual situation. if I understand it you have books that have a calibre cover already, which you want to see in your calibre library but removed from the book itself. And as you have found the only option you have to not have a cover in your book is to turn off the default calibre cover option, *and* not have a cover image associated with the book at the time you convert, right?
You should keep an eye out for the next version of the Modify ePub plugin, I'm going to push the next beta version up sometime today. It includes as of a few minutes ago a "Remove existing cover" option. So you should be able to just run that against your books, rather than reconverting them, saving you the hassle of clearing and adding back covers. You might also want to take a look at the Generate Cover plugin if you want a potentially prettier default cover in your library than the standard calibre one.
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