Well one by one a) When I open the main document it drops several subdocuments. It seem to be random which that has been dropped. b) Cross references do have issue. At the moment some refereces to figure although it is supposed to be video. It point to the correct illustration but just writes something wrong. c) Typographies... I am having like 10 versions of the same in my bar. How can I stop those from appearing?

If you are using the Master Documents "Feature", stop. Copy each subdocument without the final paragraph mark, into a new fresh document. Read the link. If you still have some of your work, you got lucky.

Ah let's be brave. I have done it work for many years, crashing servers without backup and survived anyways. This is just my Ph.D. I will manage that as well. So instead of saying that the system is flawed (it is, but what system is not) let's go into so more serious debugging. Well maybe I should drag it into Word Perfect so I can work on the codes https://www.msofficeforums.com/images/smilies/smile.gif More seriously: I can easy pull the complete document to make one huge large document, and maybe I should, but on the other hand I would like to know what is going on.

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.

I understand your desire to know what is going on. It is just that I would not do it with anything important. I have enough other things to occupy my time that I will wait until someone I trust says it works and then I'll use it. Steve Hudson likes to play with it as well. I recommend reading what he has written if you want to learn more.