MS Word Master Documents

I have been working with a very large document and have broken it up into subdocuments. When I am in to master document view and open up the subdocuments the formatting it some areas seem to change. For example one line of text may be changed to adifferent font. Any changes I make to these formatting problems and save still reappear when I open the document again. I was wondering how I could get Word to save my formatting changes and keep them.