InDesign’s Master Pages are quite powerful, and make long documents easy to keep consistent. They do have their difficulties though when you try to alter items that are contained on the Master Pages themselves.

The easy fix is to select all the pages you want to alter the Master Page items on in the Pages panel (Shift + Click to select more than one, or Command + Click to select noncontiguous pages), then select Override All Master Page Items from the Pages panel flyout menu.