If you're using Epubor, you ought to investigate Calibre and the Apprentice Alf plug-ins. Epubor is built on the backs of those plug-ins. Lots of users here will knock Epubor for that reason, but Epubor does simplify things and give a simple interface.
However, you can get plenty of support on the Alf blogs for free. They were very helpful to me when I was having trouble converting a B&N comic I had purchased.
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