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You could periodically do a search on every book with epub AND azw3 formats, then deleting the azw3 version of those books:
format:"=epub" and format:"=azw3"
Optionally, add a date filter if you want to only act on books you added on a certain period:
format:"=epub" and format:"=azw3" and date:>2013-10-03 and date:<2013-11-01
Then select all, "Delete books / Remove books of a specific format", and you're done.
Obviously, a backup before such a massive action is de rigueur.
Actually, I'd recommand to first create a virtual library of the books you selected with your search, then take time to peruse that virtual library to be sure that there's no mistake in the selections. Then you delete.
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