Acrobat Pro Deleting Borders and Lines

I've been comining powerpoint slides which I converted into pdfs into one pdf document using acrobat pro on mac. However everytime I add my header and footer in acrobat prop it removes all the lines and borders within my document.
How can I stop it from doing this?
davidjamesdp

To get the links, you have to use PDF Maker. It may be that the links conversion is turned off in the PDF Maker preferences.

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