Reading Order Error

When touching up the reading order, I can select elements and identify them as a heading, text, image, etc. Sometimes when doing this, or touching up the reading order, the element that I have selected will graphically change color, sometimes becoming illegible. This stays with the document I'm working on when I save it. How can I change the reading order while not ruining my PDF?

NOTE: I create the PDF in InDesign before moving it over to Acrobat to make accessible.