Headers Doing Weird Things To My Manuscript

I am a book author. I use the automatic header function for my chapter heads. This way, when I delete or add a chapter as I revise, the chapters automatically renumber and I always have a clean, accurate TOC to click through in the left margin. 

I wonder if an error or bad formatting or something like that could cause this error: I opened up my finished manuscript for revision and two chapters, more than 100 pages apart, just switched. This couldn't be a manual error. I never switch chapters like that--everything is painstakingly organized well in advance. Also, all my other changes, such as sentence edits, were marked in track changes, which I always have on during revisions. Why would this move NOT track like all the others?

Any idea of how this might have happened? A very difficult switch without my knowing or realizing AND bypassing the tracked change function? The switch was absolutely perfect, not even leaving any extra space. It would take me a long time to do that manually. Would a heading formatting error do that? Not to be paranoid, but could someone have done this remotely? I just want to make sure this doesn't happen again.