Large documents such as a thesis are often written using a separate document for each section. EndNote's CWYW function will insert a reference list at the end of each document. You will ultimately want to produce a single document that incorporates all of these chapters, with a single merged list of references.

• Create a new document and Save it, e.g. thesis_combined.docx
• Open each chapter in-turn and from the EndNote toolbar in Microsoft Word, select Convert Citations and Bibliography > Convert to Unformatted Citations. The formatted in-text citations will be replaced with unformatted citations, eg. {Brown, 2007 #34}, and the list of references will disappear
• Select all the text in the chapter, then copy and paste it into the new document in the required location
• After pasting the text into the combined document, close each chapter without saving the changes.
• Save the combined document
• Open the combined master document, eg. thesis_master.doc, and from the EndNote toolbar in Microsoft Word, select Update Citations and Bibliography. EndNote will format all the references in your document and create a single list of references at the end of the thesis
• Save the changes

Note: You may wish to take this opportunity to insert section breaks between the chapters in the combined document.