Longtime user, first time poster, as they say.
Using InDesign 5.5, I am creating documentation for a software product and I have about 1600 pages of documentation split over three volumes. I'm using the Book function and to start with I have three standard documents in each book - ToC (with front cover), Intro, all the chapters as separate documents, then an outro (with outro text and back cover). I have use a single document as the basis for all these documents, which was created based on a previous version.
Most of the chapters work well, with their contents getting put in the single ToC at the start of the book however at the end of the PDF I have several bookmarks that are taken from the original document that I used as a basis. It isn't going to be easy to talk about this in the forum without showing you at least the PDF, but I'm not really willing to post my work online directly since it is commercially sensitive.
Attached is an image showing the Bookmarks panel of the PDF for one of the volumes, but since all are based on the same initial model document, all three have the same problem to a lesser or greater extent. You will see several "Introduction" groups that contain the same info as the ones that are opened.
Clicking on the bookmarks in these repeated Introduction bookmarks takes to the "right" place in the document in the sense that they are legitimate Introductions, just not a single generic bookmark. That's to say that although the bookmark text is repeated, each one takes you to a different introduction.
I've had a look in the binary for each document file and effectively there are mentions of things like "Preparing the Hard Drives for Basic Network Rendering", but there aren't in the docs inside InDesign or using Ctrl-Y (just in case).
Replying to my own question, I'm sure this is just a patch over the problem rather than a resolution, but I have found that if I go to the page indicated by the "false" bookmarks and actually create a Table of Contents that I place off the page so it won't be seen in the PDF, all is well.
Posting this in case a) someone can give me a more correct solution and b) to help anyone faced with the same problem.