Quote From timefortea:
What can possibly go wrong!!?
Lots! Unfortunately it's impossible to predict what exactly.
I would strongly recommend going and having a look at whatever your uni's thesis presentation regulations are e.g. with respect to font size, type, margins, whether you can do it double sided (in which case you might want to look at how to do 'mirrored margins' so as not to waste space).
Then open a fresh Word doc, and apply all the relevant formatting to the blank doc before you paste anything at all in. This includes making sure the 'Styles' for headings and subheadings meet your requirements. Then, when you paste in, use the 'paste special' option, and your text should adopt the formatting of your master document, rather than whatever it was before. You might still have to reapply heading styles, but at least the body text should fulfil whatever your specifications are.
Good luck!