I need to do a bit more testing, but from what I have seen so far the problem appears to be in calibre conversion's handling of EPUB3 nav documents.
If the nav document is not in the spine of the book calibre changes its location to the root of the EPUB. When it does it it updates the links in the toc section to reflect the new relative location of the documents it points to. However it leaves the links in the landmarks and page-list sections unchanged so that they become broken in the process.
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