Are both bibliographies “a field”? It is really hard to trouble shoot these without seeing the actually document.
So you may want to start by reaching out to tech support. (www.endnote.com/support) )
But if you want to trouble shoot first - yourself.
A couple steps you can take are to first back up the current document and keep the original in a safe place.
If you put the cursor in each of the bibliographies, do they turn"grey" indicating they are an endnote generated “field”.
Another way to check is to can ask word to “view” field contents and see if all the citations and bibliography turn into giberish. (shift F9 on a PC, repeating will restore them to “normal”).
If they are all still fields, try this:
“Convert to unformated citations” (from the endnote toolbar/ribbon)- and see if all the citations themselves are converted to curly bracketed {Author Year, #rec no} and have both bibliographies disappeared?
If one or both bibliographies are still there and everyone has “unformatted” then delete any resisdual bibliographies and try to “udate citations and bibliography”. This should produce a new bibliography at the end, and you can drag and drop it to whereever you really want it to be. (DO NOT TRY to Cut and paste, as it will reproduce the bibliography in the same location, before you can paste it elsewhere, but you can turn off auto formating from the endnote ribbon, to avoid this. Remembert to turn it back on though.).
If only some of the citations are converted - they they may have been delinked from endnote and converted to plain text. This can happen if the document was opened in another processor, other than word or Pages depending on what you use. You cannot switch between processors, as the fields are then lost. So if you supervisor openned it in OpenOffice, for example, those linked fields are lost.
If this is the case you will need to reinsert those by some mechanism which can be automated to some extent, based on the output style you have been using (numbers? author, year?) but is cumbersome.
Another caveate is that if you are using endnote online, record numbers may have changed over time and endnote will ask if each citation is the correct citation in your library. – To avoid this, before you “convert to unformatted citations” you may want to first change the termporary citations to use another field, like page numbers, if you may have an online library that may have altered the record numbers over time. This setting is in preferences – that is why you backed it up -so you can go back and make another copy to try this on!]
or you cna PM me and I can try to look at for you maybe on dropbox or google drive, but I have no association with the endnote tech support, I am just a user.