Let's be clear here. Master Documents can corrupt parts of your thesis that are not even open. Yours would not be the first! It can get your backups! Read the page I gave you. The language "The jury is in: The Master Document feature in Word 2010 remains word processing's answer to Conan the Destroyer. Use it only if you enjoy pain and frustration." is a direct quotation from the Microsoft Word 2010 Bible.

AFAIK, the MD feature in WP works. The one in Word has never worked, it may never work. It was introduced into Word flawed so Word could say it had the same feature as WP. They have never managed to fix it and I do not know that they have tried all that hard.

Having it all in one document works.

If you want a document assembly engine that can put together disparate parts of your thesis, take a look at Graham Mayor's Boiler Add-In.

Sorry, but I learned as a child to not play with fire. I still enjoy a campfire but I don't light one in my living room on the floor.