Headers/Footers from Word to PDF

I have 2 Word 2003 docs. Both have header (with logo) and footers.
I am combining them into one PDF. When I add a footer for page numbers in the PDF the logo disappears in on one of the docs, but not the other.
I have tried creating the PDF of each doc individually and adding footer for page numbers.
Doc 1: Adding footer for page numbers works fine, logo stays in header.
Doc 2: When adding footer for page numbers, dialog box appears asking if I want to override the existing header/footer. I click yes, the page numbers go in fine, but the logo disappears.
I have figured out how to use "watermark" in Acrobat to replace the logo, but it won't work on the pages that keep the logo from Word.
I don't want to remove the logo from each of the Word docs.
How do I accomplish having page numbers AND logo in header of final PDF?
Thanks very much
w

The problem is that if I add the page numbers to the Word doc, they keep the individual page numbers of each doc once combined into the PDF.
I need to apply the page numbers based on the finished PDF.

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