Doing a Calibre conversion of ePub > ePub especially for sale is a really bad idea.
You want HAND CRAFTED eBook for any eBooks you are going to sell. You do not want to rely on any sort of conversion. Use Calibre's eBook editor or Sigil to edit your ePub and get rid of anything that comes from a conversion. This means you might have to completely redo the entire CSS and every single class in your eBook. But that's OK. It will be a better eBook when it's done.
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