TechWhirl (TECHWR-L) is a resource for technical writing and technical communications professionals of all experience levels and in all industries to share their experiences and acquire information.
For two decades, technical communicators have turned to TechWhirl to ask and answer questions about the always-changing world of technical communications, such as tools, skills, career paths, methodologies, and emerging industries. The TechWhirl Archives and magazine, created for, by and about technical writers, offer a wealth of knowledge to everyone with an interest in any aspect of technical communications.
Recreating all the bookmarks for such a large document does sound like an
extremely tedious task. I convert FrameMaker documents to PDF often and
fortunately do not have to recreate bookmarks each time I distill a document
(Frame does this automatically).
Have you tried posting your question to the PDF mailing list? It really helped
me out when I first started using Acrobat. It's also good for asking advanced
questions. Feel free (you and also other TECWR-L subscribers) to email me if
you'd like me to send information about that list to you.