Acrobat User Community Forums

Navigation is the big issue. How are you opening these files? with direct link? Direct links are subject to the version and preferences set by the user on thier system.  Sometimes links open in the same browser window as your app, sometimes in a new window, and some times in a standalone Acrobat.  This also poses problems for cross linking between PDF Help files, and getting back to your Java application page and possibly loosing your session info.

You can get better consistancy by using the HTML Object tag to force the PDF to display in a frame or new window.  Also, if you make all links in the PDF and the Java Help menu call a server side script (rather than link directly to a PDF) you can have near total control over how PDFs are handled in the cross linking.

But the main point is to make sure the cross linking between documents doesn't confuse or loose the user, or obscure your application. 

Almost forgot, there's also a performance issue with PDF. The help files should be small and linearized (i.e. web optimized).  It's often useful to have video presentations embedded in the PDF.  If you do this, then make the actual media files web links.  Don't embed the media into the PDF.

Cheers,