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The epubcheck plugin installs in the calibre ebook-editor not in calibre itself.
What one friend of mine did was to create a custom column (integer format), selected all the books that Quality Check showed as 'version="2.0"' and entered a 2 in the column using the metadata edit in bulk option. He then selected all books with a 'version="3.0"' and entered a 3 in the column. Oddly, he did find a couple of books that were supposed to be epub but did not have the version number when he sorted on that column.
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