My solution would be to use a USB stick rather than a CD. Then you can use the USB as a drive, work directly from the USB rather than your "work folder" and make your hyperlinks relative to the root directory on the USB drive. Then PDF it and you should be ok as everything is on the root. USB drives for the sort of size of your docs are pretty cheap these days and don't get scratched!! My customers prefer them anyway. But if you really need a CD then copy the root from the USB rather than your work directory as the burn data! Put in an autorun and there you go!

I have done this quite sucessfully with a Excel database linked to a PDF through hyperlinking