Can't get Table of Contents to Include All Chapters

[CrossReach]

HI,



I'm editing a Bible. It has over 1100 chapters. I used Find and Replace to make the process much faster. I only had to change 66 chapters this way rather over 1100. But it seems to have messed with the document somehow. Now only chapter one of each book is recognized by the automatic TOC thingy. The last thing I want is to create a manual TOC of 1100 entries...

All the chapter headings are under Style Heading 2. As you can see from the file I have attached, when I select one of the others chapters (say Genesis chapter 2) and press Style Heading 2 again, it selects all of the text. So there is some weird mix up having gone on here. Even selecting chapter 1 and pressing Style Heading 2 does something weird to it, though different from all subsequent chapters.

Hopefully this is confusing to someone and they can help shed some light on the issue. Any help with this would be greatly appreciated.