Keep each chapter document separate until the very end when you no longer wish to make any changes to your EndNote references. You will be combining them for printing/submission purposes only.

• Open each chapter document and in the EndNote tab of each click on Convert Citations and Bibliography > Convert to Plain Text
• You will be warned that this will create a new copy of your document stripped of all EndNote markers. Click on OK to continue
• Copy and paste your documents together into one final document

Your final document will retain chapter bibliographies.