If you have created separate chapters for your thesis or dissertation and each one has references in created using EndNote then once you are ready to merge them in one final document you will need to take the following steps to ensure your references display properly

• Create a new blank document where you will place all the chapters.
• Make a backup copy of all the chapters you wish to merge.
• Open the documents to be merged in Word.
• Copy the text of the individual documents, but NOT the reference list.  It is important that you do not include the reference list in the text you copy.
• Paste the text of each document into the new blank Word document.
• In your new document with all your chapters merged choose Update Citations and Bibliography on the EndNote toolbar in Word. 
• Your list of references (everything that has been referred to in your document) will appear at the end.