How to combine bibliographies

I am writting my thesis in seperate chapters that I want to combine into one final document, how can I have the references at the end of the master document without duplicates rather than at the end of each chapter ?

First, make backup copies of your chapter files - which is always good practice when working with important materials.

Then with one set of your chapter files, unformat the citations in each chapter which will replace the in-text citations with temporary citations (curly brackets).  Next, append each chapter to create one document. Once the document (encompassing all the chapters) is completed, format the citations to replace the temporary citations and generate a complete bibliography.

Working with master documents that already have already been joined with the generated reference list, I find that it is easiest to go thru and manually delete the list from each section, and then reformat ensuring you are using a style that doesn’t insert a reference list in each section.  -Alternatively go to the individual chapters and save them unformatted and then format the master document. 

Of course CrazyGecko is correct.  You should have all the files backed up - but  despite my historical horrible memories of Master Documents in earlier versions of Word, several of my students have been using that to create their multi-chaptered thesis, and we haven’t really run into any serious problems - once people know what they are doing! My students work on the separate chapters, and this updates the chapters in the master document, but they usually work with CWYW off, so the generated bibliography doesn’t complicate things in the master document.  Then we format when we want.  Incidentally, we also tend to turn off the hyperlinking of citations to the reference list until the final versions.  It is nice to have a hyperlinked PDF at the end for the examiners!