Indesign question: Master page items I remove won't stay gone

I'm working on laying out a book, with various chapters which are separate files. Naturally there's a master page with various guides I use a lot, as well as a fairly standard running header with page numbers and chapter and section names. As is standard practise, I want these to appear on nearly every page, but not on the first pages of chapters. (There are other times I might want to override this, but that's the main one.) So, I Ctrl-Shift-click and delete them when I set up a new chapter.
Problem is, they don't stay gone. Every so often, I open up a previous chapter and find that these elements are back on the first page of that chapter, and I delete them again. I've only been noticing this since I made the chapters in question into a book file so I could keep an eye on my page count and synch up styles more easily.
My best guess is that maybe it has something to do with the aforementioned synching. I do want those chapters to share the same master page(s) but do not want IDto keep reapplying elements from them to individual pages that I've already manually removed them from (sometimes more than once). How can I prevent this from happening? (Or alternatively, if this isn't the cause of the problem, what else could it be and how do I deal with that?)

Fair enough. Guess that's just as easy, if not slightly easier, than what I've been doing, and so far it seems to be working.

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