Thanks for the response. I did try knitting / building multiple times. And yes, my local book was different from the one uploaded to bookdown.org. The local book looked fine, links worked fine.
To explain how I changed my book, I combined chapters 1 and 2 into a new chapter 1. I also changed the name of header one (#). Then I moved the content from chapter 3 into 2, chapter 4 into 3 etc. I also added #labels to each header one for all chapters so I could cross reference from within the book. The chapter names are all multiword phrases but the labels were boring: chapter1, chapter2 etc.
What was interesting is that I could find the old chapter 1 AND the new chapter 1 by replacing "chapter1" in the web address ("XXX/where-are-genes/chapter1") with the new or old chapter name (i.e. new chapter name: "XXX/where-are-genes/genes-genomes-and-genome-browsers" ). So yes. all the files were in bookdown.org but the link in the TOC of the book was not working because it was using "XXX/where-are-genes/chapter1" as its web address instead of what actually worked: "XXX/where-are-genes/genes-genomes-and-genome-browsers"
Anyway . . . I FIXED the problem by getting rid of the {#label} for chapter one, header one. This doesn't make any sense to me but I knew I didn't need it since I do not cross reference chapter 1 anywhere in my book. So problem solved but no idea why.