This question was posted in response to the following article: http://help.adobe.com/en_US/indesign/cs/using/WS6CF1F6DA-7863-49cd-9A5A-AC656D630DFA.html
I use Package Book for Print when I export a book and its chapter files to create a new similar technical manual. This exports the links for graphics and correctly updates their references to use the new folder. HOWEVER, it does not update the cross references to use the documents in the new folder. As I still want these cross references, the only solution I have found is to open each cross reference and then browse to the file in the new folder for its cross-reference. Nothing is changed except the path to the new folder, that does not get updated. (I reported this as a bug, but received a reply that it is not a bug--though I cannot see why this would be intentional.) Updating hundreds of these links is a painful process, as it does not appear there is any way to just reset the path for the cross-references, each one must be done by hand. Does anyone have a good way to do this? None of the tools mentioned here let you fix these links, as they are not broken, just not set to the correct directory during export.