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Personally, I would do a search for all books in both epub and mobi formats (the formats:EPUB and formats:mobi search suggested by @theducks). Once the search has finished, select all the books, right-click, go down to the Remove books menu item and hover until the sub-menu pops open. From the sub-menu, click on Remove files of a specific format from selected books. From the pop-up, double check that the count for ePub and mobi are the same, hightlight mobi and click OK. This will remove all the mobi books where the same book exists in ePub format.
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