"Fix" is to recognize that read order has nothing to do with an accessible (ISO 14289-1 compliant) PDF. Ensure the PDF has a symantically proper, well-formed structure tree. That is what assisitive technology (AT) applications parse.
It sounds like you are working in the Order panel. I find the Order panel to be a frustrating and inaccurate tool. I have pretty much given up on it in favor of the Tags panel. Provided that the tab order is set to “Use Document Structure” (you can check this in the Page Thumbnails panel by selecting one or more pages, right click and select Page Properties), the order of the tags determines the reading order. The Order panel works – often not very well – by rearranging the tags. You get a much finer level of control and accuracy by rearranging the tags yourself using the Tags panel. If some part of the page goes blank, objects are overlapping each other in the visual representation of the page. Often this is text on top of a shaded box. Sometimes the box is the same shade as the page background so you do not see it. Using the Shift (plus) and Ctrl (minus) keys as needed, select and tag each of the overlapping objects separately. Then arrange the order in the tag tree so that whatever went blank reappears. Once the tags are in the right order, you can select anything that does not add value in the document structure (the shaded box in my example) and tag it as a background artifact.
Hope this helps.
a ‘C’ student