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Whether using the Quality Check or Find Duplicates, you're still going to have to look through each ebook for quality control. Failure to do so means you're very likely to find that you've retained the damaged, less-structured, missing font, damaged/missing image, funky colored, whatever... version of the ebook.
Start with Quality Check and other "fill in" or "match" metadata plugins or processes. Then try Find Duplicates. Open both books, look through them and compare. Check every feature imaginable.
But believe me. One of the worse things you can do is remove duplicates too early in the library building process. Too often I've found the "obvious" choice of which file to keep to be the wrong answer. Now how do you get that duplicate you deleted six months ago back?
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