For two or three of these non-printing Footnotes, go into the proof window and click the footnote button.
Then, on the Footnote page, does the Footnote Text appear for both the Final Report and for the Research Report?
Perhaps the footnotes have only been created for the Research Report? If so, change the radio button to Final Report. Click the All Evidence or Selected Evidence button to transfer a copy of the the Footnote text to the Final Report Window.