While I am formatting my indesign file, sometimes removing pages or adding them throws neatly formatted text off the margins. Why
1) If you have Left and Right master pages, make sure the margin is the same on both. Not mirrored (6p outside/3p inside), but the same (3p all around).
2) Make sure you don't have text boxes leaking onto the pasteboard; sometimes that makes text boxes fall off when you rearrange things.