Andrew's solution sounds like a good one. I have had that problem but was in a way fortunate that those docs still had manual double spacing between paragraphs. So I have a macro that replaced ^p^p with a nonce string (@@@ usually), then every remaining ^p with a space, then the nonce string (@@@) back to the two paragraph breaks.

You can use find and replace for the string that shows up as the old header and footer if those have moved to your regular text. Our PDF's from 10+ years ago had been made in WordPerfect, so it didn't seem to preserve header and footer separation. And it really did a number on old PDF'd sections that were two columns.