There is no evidence of that in the code you posted - all it does regarding bookmarks is to delete them. It's not apparent what point that serves.
The proper way to modify font attributes and the like, especially when you're dealing with an entire document, is to redefine the Styles it uses or to define and apply an appropriate Style - not to use brute-force overriding of the existing Style definitions. Assuming your existing document is using Styles properly, that obviates any concerns regarding headers & footers.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]