A couple of thoughts that might make your journey last longer before the crash:

Every document (Master and sub) should be based on a single template that has your styles. All formatting should be done using those styles.

Numbering must be linked to styles as described in How to create numbered headings or outline numbering in Word 2007 and Word 2010. Using numbering on the ribbon buttons will result in scrambling in a large document.

Do not edit subdocuments from the Master Document interface. Use it only for printing. Do not save any editing of subdocuments at the Master Document level.

Read http://techwhirl.com/wp-content/uplo...masterdocs.pdf. It will give you the best chance of survival.