So I think I have the solution that you are looking for. I don't know if it was added in more recent updates or what, but it works. This is in regards to editing a word heavy document with flowing text, such as a long novel:
1. Create text boxes on your master pages, one on the left and one on the right. Link the left box to the right box on the master pages. After this, you will NOT edit the master pages any more, unless you later decide to resize the boxes.
2. On your actual pages, paste or place your first chapter into the first text box. (Note: do not create any new, empty pages, intending to fill them).
3. Shift-click on the box's text-linking triangle. This will create new pages and fill them with the flowing text.
4. If it ends on a left page, and you want your next chapter to start on the right page, unlink the text boxes, then paste your next chapter into the single text frame on the right and repeat the process.
Now if you want to edit your margins by adjusting the master text boxes, all your pages will reflect the changes. If you do make changes, you'll have to go through and check the end of your chapters that no text is missing since you adjusted everything. You might have to manually add pages and text boxes to show the hidden text after you adjust the master pages text box size, or even delete any empty pages, depending on the adjustments to the master that you make.
