Edit 11/28/2017: Also read THIS more Recent POST.
There isn't an easy button to just eliminate shared coordinates in a project. You can move the Survey Point back to the same spot as the Project Base Point and then use Specify Coordinates at Point to reset the coordinates the file is using. Sounds like I just countered my first statement?
I'm referring to the relationship between files when you use Acquire Coordinates or Publish Coordinates. Once two files are sharing coordinates you can't really remove this relationship. If you remove the link and import it again (Auto - Origin to Origin) the relationship survives. For example you can try to Acquire Coordinates from the file again to "reset" them and Revit will say that it is already sharing coordinates with the file.
To remove (really more like replace) the relationship I use a new (empty) file that is based on the stock Revit template default.rte. I import this file and Acquire Coordinates from it instead. Revit can only acquire coordinates from one source file so using a different file resets it to match this new file. Now it is possible to acquire them from the original file after removing the C/M relationship.