Excerpt from:
https://www.mobileread.com/forums/sho...d.php?t=159198
5. Now you will see you have a whole list of xhtml files, one for each of your TOC items.

Down at the bottom of this list you have a generate TOC from headings button, press it. Now check the boxes of the items you want to appear in your TOC. When you close this window you will now have a TOC.ncx on your list. This will convert just fine to any format. You can also click on the ncx file and edit what apears on your TOC. Just now it will probably only say "Chapter one" for instance. Just put your cusor inbetween the two chevrons and you can edit the entry to, say, "Chapter 1: A Strange Affair" or whatever. This will now appear instantly in your TOC. Note: If you have no entries in the generate TOC list you need to go back and highlight each chapter heading and select H1 from the little drop down at the top left of your screen. Try again and the chapter names should be on the list.
Hope this helps. Using the generate button at the bottom left will completely re-write your TOC into a well structured ncx file.
Good luck