Originally Posted by Points
I realize this is an old thread, but I'm having the same problem. Which subdirectory? I've looked in every relevant one (there aren't that many) and don't see it. It's not in the zip file, the author folder, or the book-title subfolder. Kindle viewer and Kindle for PC do show a toc.ncx, but it's just not there as a separate file.
This is one reason you don't resurrect old threads. This thread is about ePub books, but you seem to be asking about some sort of kindle or mobi book?
I checked 20 random ePubs that had been converted using calibre and all of them had the content.opf and the toc.ncx files in the root of the book.
I believe Mobi files are different and the toc is actually located in the regular html of the book at the back of the book.
If your question isn't about ePubs you might want to start a new thread with an appropriate title and all pertinent information.