TOC for book partially breaks bookmarks

Are you, per chance, running multiple tables of contents?

I've previously run across similar issues when running separate tables of contents for books (e.g. - one for chapters, one for technical illustrations/tables/photographs, etc.). Creating and placing multiple tables of contents is easy, provided you leave the Replace Existing Table of Contents check box unselected.

In the layout/text context, running multiple ToCs appears seamless. But there's a lot of metadata work that happens in the background that seems to get scrambled hopelessly for other contexts. At its most basic, the only problem you'll have is that the last ToC you run within InDesign "wins." However, it can also scramble things from previously built ToCs like PDF bookmarks and other text tagging for electronic publication.

I haven't found a "fix" for that, but I have had success with a work-around. The last ToC I run is for the most prevalent function (generally, the book chapters) and then I double back and check all the bookmarks within the book through the Bookmarks panel (accessible through the Window>Interactive>Bookmarks menu command) and clean up/replace any anomalies I find independently from the ToC automated bookmarking functions.

In short, with multiple ToCs, I can't — and don't — rely on InDesign's automatically generated PDF bookmarks functions to get me what I may need, and find that I have to rely on my own attention and skills to get the results I want. Wish I had better news for you, but this is the best I've got.

Hope this helps,

Randy

Re-checking obvious things is always a smart move!

What OS version? What version of InDesign patch?

Did you experiment with washing the INDD files out to IDML and back?

Did you also check ON the easy-to-miss "Include Book Documents" in the ToC generator dialog box (where the documents are open and also the book file)?