Doctoral Thesis--Chapter format and merging

Assemble your document in whatever way you have planned, inserting section breaks (Next Page or Odd Page) between chapters. (For help with page numbering, see http://www.word.mvps.org/FAQs/Formatting/front_matter_2007.htm.)

Then, on the References tab, in the Footnotes group, click the dialog launcher (the small arrow in the bottom right corner). Select the radio button for Endnotes and change the setting from "End of document" to "End of section." Note that, if any chapter has internal section breaks, you'll need to suppress endnotes (Layout tab of Page Setup dialog) for the sections before the last in that chapter, and there is no way to restart numbering by chapter in this situation because note numbering can be restarted only by section, and Word takes that very literally.

If you need a TOC or index, you'll find it much simpler to handle the thesis as a single document, despite the drawbacks. This also facilitates converting to PDF with links intact. Unless Foxit offers benefits over Word's native PDF-creation feature, you may want to use the latter.