1. Master/sub: See Master Documents "Feature" now!
2. Numbering - use the methods set forth in How to create numbered headings or outline numbering in Ribbon Versions of Word by Shauna Kelly and make sure you use the same styles in all of your documents.

Make individual backups of each part of your Master document. Store those backups off-site and not on your network. The Master document feature in Word has been known to corrupt parts that are not open including backups that are locally stored.

If you are not using the MD feature, but just those terms, I apologize for sounding alarmist. If you are, though, I would urge you to cast a vote here:
https://word.uservoice.com/forums/30...cument-feature