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I run multiple count pages on small batches of books all the time. Very occasionally I get race condition where the count pages initial dialog box gets lost and won't go away, but that's the only issue I've seen. This problem might be worse if you run a separate count pages for each book, all in parallel.
I'd be tempted to select all the uncounted books and run a single count pages job, except that occasionally some large book gets stuck and never finishes, and then all the counts in that job before it are lost.
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