In FSX and Prepar3D-based flight simulators, the navigation aids such as VORs, NDBs, and ILSes are built into the sim's core scenery. If any of the these items have been changed or decommissioned in the real world, then the simulator's underlying scenery needs updating. This also applies to runway designators.
RealNav Data is strictly an database of procedures (SIDs, STARs, Approaches, and Airways) that GPS simulations utilize for displaying the proper procedures, but RealNav Data does not (currently) change the simulator's core scenery.
If you are using Prepar3D in a professional simulator, you can contact the simulator manufacturer to see if they have a scenery update available for the navaid that interests you.