When you delete section breaks, the section formatting flows backwards towards the top of the doc. So if your section breaks are right next to each other, deleting a section break flows the page setup backwards until it hits another section break.

If removing the extra break removes the page format you want then:
Swap the position of the section breaks BEFORE deleting the break you want to remove. Do this by selecting it and dragging it to the other side of the other break. Then remove the break you wanted to remove. You probably also then need to change the type to 'Next Page' to finish off the last step.

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Andrew Lockton
Chrysalis Design, Melbourne Australia