Disappearing Headers and Page Numbers When I Change Paper Size

It's not completely clear what your process is, but I'll note a few things:

First, master pages are now parent pages. May as well get used to it. 🙂

If you make a page smaller, elements like boxes for the header and footer can end up off the page and on the 'artboard' area. You should be able to see them if you zoom out a bit.

If reapplying the parent page restores the header/footer, simply reapply it to all your pages. Any number of things can cause pages with the wrong parent (such as 'None') to multiply in your layout. You may have inserted a page and inadvertently not selected the correct parent for it, and the faulty layout expanded from there.

And just a hint, don't apply page-specific master pages until you're right at the end. Applying a blank master (without header or footer) to, say, a chapter title page will often go wrong if the page flow changes — a text page where the chapter used to start will have no header and the chapter title page will. There is, unfortunately, no way to anchor a page format to a header or section break or the like, so you have to make one last pass through to apply things like chapter-start page formats.

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