In wanting to have better control over a ToC, I thought to use hidden, non-printing text layers to create the ToC entries. There would be one hidden layer per chapter (InDesign document).
This actually works to make a nice ToC, but the issue is that when exported for Kindle, these hidden layers show up in the book.
I've tried using white text and no-ink on these, and this does hide them for some versions of Kindle; however, the text is still displayed on older versions.
I am having the exact same problem and no one seems to know what to do. Did you ever figure this out?