When I export a large book from CS6 to an interactive PDF, the bookmarks are jumbled. Many are missing the chapter heading so the levels within those chapters are thrown off and some chapter heading appear as a lower level at the end of the previous chapter. The last seven chapters appear at the beginning (in reverse order). The contents within those chapters seem to be in correct order. There are also capitalization issues.
The book is made up of 38 documents (Chapters) and is 584 pages, with appx 1860 Chapter headings and subheadings that should appear as bookmarks. I have tried changing things in the main documents but that doesn't seem to change even the cap problem.
Where is the PDF bookmarks generated from in InDesign and can I fix it before exporting because I don't really want to have to reset 1860 bookmarks in Acrobat?
There are two ways to create bookmarks from InDesign: (1) Manually from the Bookmarks panel, or (2) creating a Table of Contents in Layout > Table of Contents. The bookmarks should be generating if the checkbox for creating PDF bookmarks is checked, by the way you've set up the TOC. You can set up levels of bookmarks there.