I maintain a large manual. In the past I used Word 2003, converted the chapters and annexes into PDF. I merged the various PDF files into one document and the bookmarks worked fine. I received a new computer with Word 2007 and Acrobat 7. Now when I convert the various manual files from Word to PDF, the bookmarks in the individual PDF files look and work fine. When I merge the files into one large PDF file, the bookmarks look find but they only work for the first file, after that they they do not take you to the correct location.
Acrobat compatibility/support for Office 2007 applications began with Acrobat 8.1
(prior releases where "on the street" before the release of Office 2007).
Be well...
Be well...