The fact there's so much layout change - as well as the image duplication - suggests there's content preceding the pages in your screenshots that is suppressed until you do a print. Conversely, the radical change in overall page count suggests document corruption.

For the latter, you probably wouldn't need to endure "long process of copying and pasting bits of the document, reorganising the references, heading styles, etc." Rather, corrupt documents can often be 'repaired' by inserting a new, empty, paragraph at the very end, copying everything except that new paragraph to a new document based on the same template (headers & footers for the last Section may need to be copied separately), closing the old document and saving the new one over it.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]