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I've seen it fairly often.
There's not much you can do about it; it's caused by the program that creates the PDF in the first place. The headers & footers are inserted into a different spot in the workflow from the main text; it's as if either they're created first on the page, and then the text is inserted, or the text is placed on all the pages, and then the headers are added by the program.
Reflow puts them in the wrong places because the coding puts their order in some weird spot it can't understand.
I've had some luck at cropping the page (I use Acrobat Pro, but there's free cropping software) to hide the headers & footers, and then convert. Sometimes that keeps the conversion from seeing them.
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