I have a document set up with a bunch of conditional text - enough that when I change a condition there is always a change in page count. I decided that I needed a running header change for everything but the first page, so I copied the first master (where Smart Text Reflow worked), made the header modifications and added it to the second+ page of my document. Now the text boxes will add pages but not subtract them, and with the number of documents I have to export, this inconvenience is too great.
I have Smart Text Reflow set to 'End of Story', Limited to Primary Text Frames, and Delete Extra pages. No idea what's wrong.