Acrobat conversions to Word typically put 'header' and 'footer' information into the body of the document anyway in my experience. This is because the structure of an acrobat document doesn't usually contain a physical header or footer - it is just more unstructured content on the page.

Perhaps you could explore the conversion options of your PDF>DOCX conversion to see why content is told to go into a header/footer.

I'm also unsure why you think it is a good idea to convert to Word when your data analysis could also be done by processing the PDF file - why change formats when Acrobat is also programmable?

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Andrew Lockton
Chrysalis Design, Melbourne Australia