I've set all my sections in a book layout (by chapter). This retains the proper flow of page numbers and running heads, and that's all great. If edits to a section of text cause the chapter to be shorter or longer, the pages naturally reflow (text flows continuously throughout doc), but the Master Pages do not re-position (particularly in the case of part or chapter openings, which are styled differently) ... so, I then add or delete a page, or re-place the master in the appropriate spot.
I have someone learning to edit my documents, who comes from a Word background and is asking me why master pages end up in the wrong place when a change is made, and I don't have an answer for her. To me, a change to a section naturally affects the flow of the document – am I missing something? (Hope I explained this this so you understand!)
Because in InDesign, master pages are assigned to specific page numbers, and not to the content. As the content reflows, the assigned master pages remain on the original pages.
There is a feature request to attach master pages to paragraph styles so that they can move with the text reflow, but as of now it still is not part of the software. Perhaps both you and you colleague will consider voting for it.
So I wasn't losimg my marbles, after all! Thank you, it's just as I thought. And I just voted!
Check out this addon:
You can apply parent pages based on paragraph or object styles.