We've encountered a couple of projects that show us this error (attached) every time we sync our files. This latest one just started doing it randomly after we added a design option. It prompts us for every instance of a link and every time we save to central. How do I make it stop? 
I found the following document regarding this message:
Location Position Changed dialog when saving in Revit
http://usa.autodesk.com/getdoc/id=TS14334953
I also found the following forum thread regarding the message (with Revit 2010):
http://forums.autodesk.com/t5/Autodesk-Revit-Architecture/Revit-2010-Shared-Coordinates/td-p/2558246
