Need help understanding how the Headers / Footers work in a Word Reporting Package

Summary: I have a large Word-based Report Package (150 pages) with non-continuous headers / footers. The headers are different for each section of the report and therefore utilise the "different First Page" option in Word. The footers have page numbers and "different even/odd pages" is also active for alignment purposes. This report is published to the market and highly scruitinised, and so standards are extremely high.

Despite having a doclet correctly set up for every section, as well as the doclet before it, when stitching the doclets together, there are often incorrect headers / footers or they'll be missing completely. Since the report contains more than 200 sections, it's difficult to troubleshoot every section in every doclet.