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One thing you can do (even with the DRM in place) is unzip the ePub in the Finder, and then use the "ePub Zip" script that can be found elsewhere on the site to re-zip it. It works like a charm for some of these files, for me anyways.
A corrupted directory in the ZIP just means it needs to be re-zipped. As the DRM is inside the ZIP, you can unzip and rezip without mucking with the DRM involved.
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