PROBLEM:
After Publishing Coordinates to a linked file Revit will not let you save that linked file.
You get the message:
Error: You cannot save the link because it has changes in more than just shared coordinates
CAUSE:
This is a bug in Revit. Possibly a problem with network settings.
SOLUTION:
Make sure you have an up to date Local File of the linked filed on the hard drive of your computer.
In the host file (where you Published Coordinates) under Insert tab in Manage Links dialog use Reload From... to reload the linked file from the Local file you have on your computer.
Publish Coordinates to the linked file.
In Manage Links dialog select the linked file and and hit Save Positions button.
Close the host file.
Open the Local File (on your hard disk) of the linked file.
Synchronize with Central.
Close the Local linked file.
Open the host file.
Under Insert tab in Manage Links dialog use Reload From... to reload the central file from its location on the server.