I may get to your question at some point but expect someone else will answer before I sort it out.

In the meantime, it is vital for a thesis that you set up your numbering using the methods shown in How to create numbered headings or outline numbering in Ribbon Versions of Word by Shauna Kelly. You want to do this early rather than late. Numbering created by simply clicking on the buttons will be a disaster.

Second point, do not use the Master Documents "Feature". More than one thesis has been completely trashed by that "feature."