I'm going to put this in under 'wishlist' rather than bugs because an argument can be made for the behavior described herein. I don't think it's a good one, but it's at least plausible.
I have been moving some content around between chapters. I have multiple story threads, and changes in the weight given to one episode or another are driving the reordering. In the process, I exchanged the places of a couple of chapters.
There are also inactive previous versions of a couple of chapters. I stress that they are inactive. They had the same numbers as a couple of the active chapters. The renumbering caused first one of them, and then the other, to be given the number of an active chapter. That change the number of another active chapter, triggering a chain reaction. I don't know if I've gotten it straightened out, since my laptop battery ran out when a five-minute task took over an hour. Both the time and the battery problems were worsened by the multiple page loads I needed to get back where I was after changes were made, navigating through the edit chain from the top each time. I also found the drop-down bouncing to different spots on the page. (Sorry, I didn't think to capture screenshots. My bad on that.)
I think you have a deep problem stemming from your model of version control (snapshot vs. structure, and how to resolve the tensions that result) so I won't ask for changes there.
Instead, my request seems simple: exclude inactive chapters from the renumbering arena, so they cannot trigger chain reactions of this sort. ( It might not be simple and a different fix might be easier. But I'm trying.)