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.
To truly remove (really more like replace) the relationship I use a new 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 "good" one "resets" it ...
Revit OpEd: Shared Coordinates and Copy Monitor