Not sure why a div for columns would cause the pages to start renumbering like it was a separate section, but here's a possible work around:

What if you insert two text boxes. Using the text box tools, you can click create link to make the text from one flow to the other. Using the advanced positioning tools, you can set the horizontal position relative to margin or page. You can set the vertical position relative to paragraph so the two text boxes will move up and down as your pages change with other edits (theoretically). I often resort to text boxes when columns create other problems, but I've never tried this in long documents before.