Assuming that what you want is a single bibliograpny at the end of the book, I suggest that you unformat the references in each document, discard any residual bibliograpny and then join the chapters into a new document and then reformat assuming you still have access to the Endnote libraries.
Alternatively you could try unfomating the combined document, delete any residual bibliographys, and then reformat. then you can move your reference list to the appropriate place. in the book (if it isn’t right at the end).