First, do not use the Master Documents "Feature" in Microsoft Word.




Are your commentaries separate documents? If so, just keep them that way.
When done, save each as pdf and concatenate the pdf files.

Alternatively, have the main text and commentaries in separate Word Sections. Restart your footnote numbering at the beginning of each section and set your endnotes to be at the end of each section and restart numbering.

Thank you for your reply.
Thank you for the advice not to use master docs.
I want to keep things together. So I guess section breaks would be the most efficient way to do things.

Question:
Is there a way to set a style to force it to start a new section? I can only see that you can put a page break before a style, but don't see the option to put a section break?