Moved to InDesign EPUB forum.
Sounds like all you did was create aliases/shortcuts to the original files. What operating system are you on?
I'm using Windows 8.1. I think I figured it out though. I hadn't noticed the way InDesign kept a persistent link to the previous directories when adding/removing stuff from the book file. I had to completely rename both directories where I had my files saved to notice the difference along with having both book files open and realizing I could only open 1 instance of the actual 'chapter'.
So thanks for answering as quickly as you did. Hopefully I won't run into this problem again now that I know what to look for.
Have a great day.
On another matter, I'd put the TOC in before the Foreword (note the spelling) and the Preface. And, for an ePub, I'd put the copyright page at the end of the book.