I had hoped to put my dissertation all together as a master document. However, it just didn't work out. The picture were all messed up. I ended up cutting and pasting the chapters together, and then making changes manually. I am not sure there is a way to reliably put together a dissertation using Master documents. While it is theoretically possible, it just doesn't work in the real world. Save your work in chapters, but put it together by cut-and-paste is my suggestion. Perhaps my other suggestion would be to just do your dissertation in LaTex.
On a positive note, I have turned in my dissertation, and did so before the deadline. I have some formatting corrections to do, but they are not too big. Also, I finished my corrections for the third paper. They sent me the author proofs and I sent back a few changes. It should be published soon.
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