Word Master Documents

I know that discussions about ways to combine multiple documents into one on this forum have often elicited the dread “Master document” horror stories, but this newsletter article from Office Watch would suggest that it is worth revisiting.  

Do any usergroup members  routinely use Endnote with Master documents and do you have any stories to tell?  Good or bad?  Does it work as you would expect or are there complications.  I really want to know if I can recommend this strategy to our PhD students writing up their theses.  

I would also be interested any user experience with Master documents. My advice to postgraduate students is limited by a lack of experience with Master docs. Playing around with a small test example does not provide a lot of confidence.

In the past I have seen it work well with Office XP / 2003 and ProCite, but wonder how it might work with the options in X3 that generate separate reference lists for each section / chapter.

The move in some disciplines towards a publication / journal article model for completing a dissertation, lends itself toward a chapter by chapter construction, but some students will always ask about master documents.