Your problem comes from a misunderstanding of the anchor modes of frames.
You use To page on the assumption that it will merely allow you to position the frame in the current page. The documentation may not be clear enough about it, but this assumption is faulty.
The primary consequence of anchoring To page is to lock the frame to the absolute page number at time of frame creation, say page no. 7. Subsequently, you expect this frame to follow document editing history, i.e. to keep its relative position with regard to the rest of the document. But if you remove 2 pages before, it won’t shift to page 5, it remains at page 7; if you add 1 page, it won’t shift to page 8, it remains to page 8. It remains to page 7 even if you reduce your doc to a single page, getting blank pages in between (and you can’t delete these virtual pages whatever you attempt lest you move or erase the frame).
This would have shown up immediately in a single document. With a master, it is a little more complicated. Absolute page number is a tuple (doc, page). A master can only see pages (master, page). A page like (subdoc, 7) does not exist in the master and the frame which is anchored to it can’t show up.
Remember that positioning a frame is independent from its anchoring mode. You can center in in a page even if it anchored To paragraph or To character (but not As character).
The fix is easy: you always have at least a paragraph in you intermediate “cover” pages (e.g. the paragraph containing the page break). Anchor your frame to this paragraph.
I noticed that your copyright frame is also anchored To page, this time in the master. Change its mode because preceding pages are presently empty. This will avoid unexpected effects when you type their content.
A general remark: don’t use frame for text which is part of the main discourse development. Frames are great for side remarks, marginalia, … where the order relative to the main discourse is not really relevant. Don’t do that for elements part of this discourse like headings (which is the goal of “BIBLIOGRAPHY”). The technical order in which it is taken into account may not be what you expect, creating glitches in the TOC or other constructs supposed to reflect the order of reading.
In your case, these special paragraphs are between page breaks. A dedicated paragraph style could do the trick: horizontally centered between margins, a specific spacing above (eventually a specific spacing below if they are followed by text in the same page).
Also, use more page styles than you do: First Page us just what it tells, the cover. You use it for the cover, abstract and copyright. This will prevent you from formatting separately your cover. Index is used for all the tables, which is acceptable. Default Style for chapter content is OK, but not for the “intermediate cover” BIBLIOGRAPHY and even less for the bibliography itself.
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