First off epub files are generally pretty small but if you hate the thought of having them you can remove all files of a specific format to get rid of a bunch at once or click the remove icon in the edit metadata screen to get rid of one at a time.
No automatic solution but as it takes seconds to remove all files of a specific format from say 1000 books not a problem IMO.
Caveat: Deleting the original format will most likely come back and bite you...
Helen
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