It sounds to me like you want one big bibliography, not separate bibliographies for each chapter. Try unformating the references, delete the remnant bibliographies and then reformat the document. You should end up with one big bibliography at the end.
To “unlink” the references, use the endnote tool in word that is called “remove field codes”, or select all, ctrl+shift+f9 ON A COPY, this will remove any endnote information and make the Endnote unusable on the resulting document, but freezes things as they are. This is what you would want to do, to ensure the maintenance of individual reference lists for each chapter prior to combining.