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Modify ePub is the best option you have. If you get double covers, it is because whoever defined those ePubs did a really crappy job, and no automated tool out there is going to be able to detect that what exists in there is intended as a cover rather than "some page" in the ebook.
Use Modify ePub to get a correct cover inserted, then open in Sigil to strip out any inside covers you don't want.
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