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Very strange. I've tried it with some books: clicked the Pages field, and set it to 0. After running "Count Pages", the page count is back again where it should be. (Calibre 1.3.0, and all the latest plugins, btw.)
Have you checked that the column name is set correctly in the Count Pages plugin; i.e., is the column in there the same as the one you previously wrote page counts to?
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