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Calibre renames the original file as .original_epub, so it's a simple matter to just delete those files once you're satisfied that the newer epub is well formatted. But definitely open the book to make sure the conversion didn't mess up formatting before deleting the original copy.
If I was having that problem, I'd remove everything off the reader except for the current book I'm reading and test it awhile. If the excessive battery drain stops, then start transferring books back in smaller batches and using the reader for a bit between each transfer. That way you can narrow down which book (or books) is causing the problem.
I really wouldn't convert the entire library epub to epub and hope that fixed it.
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