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Page shuffling really has nothing to do with it at this point. In order to keep the chapter starts on the correct page I think the easiest method is to make each chapter a separate story, thus preventing a change in one chapter from affecting the flow in another.
To do that with a continuous story flowing through multiple chapters, work from the back to the front. Start by TURNING OFF Smart Text Reflow if it is on, then grabbing the Selection tool (Black arrow) and double-clicking the outport (the larger box near the bottom right corner of the frame) on the last frame in the second-to-last chapter (you can also singl-e click, then click inside the same frame). This will break the thread at that point. The text that was in the last chapter will dissappear from those pages, but the frames will remain and be threaded together.
The "missing" text is now overset and you should see a red plus sign in the outport you clicked before. DON'T click it again. Instead, switch to the text tool and put the cursor after the last character in the chapter. Press Ctrl (Cmd on Mac) + Shift + End to select all of the overset text, then cut to the clipboard. The red plus should be gone.
Put the text cursor in the empty frame where the l;ast chapter should start and paste.
Repeat until you have broken apart all chapters.
Now if you edit one chapter it will either create overset text at the end of the chapter or leave an empty page if you shorten the text enough to do that (Smart text reflow can be re-enabled, if you can stand it, and may actually add pages or remove them for you).
Thank you, Peter. I might have figured this out by the time it rains again where I live (which might be never the way we're going), but your explicit directions will be tried this afternoon. I really appreciate the time you took to walk me through it.