Ok, so vinco sent me the pdf he's having trouble with, and I can confirm that the previously mentioned regexes, which highlight the proper matches in the tester, don't remove those matches when converting.
I have no idea why, but it's definitely a bug.
Oddly, when I used the resulant epub (which still had the page numbers) as the input, and adjusted the regex to match the page numbers and surrounding tags in the epub, it correctly removed them in the output. (vinco, this is your temporary workaround solution).
So why is the syntax highlighter showing the regex matches, but the converter not removing them?
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