P.S. I forgot to say I'm using CC 2018.
Sorry, I remembered something else I should explain. I DO have an internal TOC in the InDesign file. I set it up in its own frames, separate from the flow of the book itself, so that it could safely regenerate if changes were made. But when I open the exported file, those pages that contained the TOC frames (there are three) are not even accounted for. Not even blank pages show up. The TOC is just plain skipped over, as if I'd never set it up at all. The TOC is not getting picked up during the export process, which leaves me with no interal TOC or links to my source paragraphs.
Okay, I hope I've remembered everything now!
Does the TOC appear in the Articles panel? Is it marked for exporting?
I'm not using the Articles panel for this manuscript. It is a straight text book with just chapter heads and text. Not even subheads, etc. The "bits and pieces" are not in separate text frames, other than the TOC I've placed inside the document. It starts right at the title on the title page and goes right to the last sentence in the About the Author blurb at the end. I'm creating my page breaks with paragraph styles and choosing those tyles -- keeping all at Level 1 -- in the TOC creation panel. (For various reasons, this manuscript did not lend itself to either an .indb or the Articles panel.)
I've watched videos and read instructions, ad infinitum, and am feeling like this is a bug in InD CC 2018 -- that is, if the TOC can be generated ONLY if one is using an .indb or the Articles panel, then they should say so (and fix it!), but such a restriction has not been mentioned in anything I've found as I've researched.
Moving to InDesign EPUB forum
Did you check if the separate TOC frame is not placed on the master page only or if you haven't it marked (by mistake) as "nonprinting" in the attributes panel.
InDesign creates by default an inline TOC besides the NAV TOC (when using the automatic TOC feature) and I also tested in CC 2018 and its working as expected (in a single file).
No, the TOC is not on any of the master pages, and it is not marked non-printing. It is placed on three pages between two parts of the front matter, but not making use of a primary text frame (I removed the primary text frame from these pages). I am truly mystified. I don't know what else I can do differently, and no one else has mentioned having this problem that I have heard of as yet.
I was running into this problem recently, too. I'm not sure if you found your solution, but what finally ended up working for me was going into the chapter title paragraph style, selecting "Export Tagging" from the menu, and assigning "h2" to the style. (EPUBs interpret "h1" as the title of the book, "h2" as chapter titles, and "h3" as sub-chapter headings.)
This worked for me. I hope it works for anyone else struggling with this issue!