The worldwide ICAO regulation defines runway directions with the magnetic north. Makes sense as GPS is not considered safe enough for main navigation, it's only here for additional help (in theory at least). Also traditional radio navigation (VOR, NDB) is done with magnetic directions. Changing runways directions happens sometimes, it's not such a rare event, as the north is moving on many parts of the globe (not everywhere the same though). I know of a few places here that have changed runway direction.

Anyway, it's not that much of a burden, because there is a very defined and safe process for updating airport and airspace data. When that type of change happens, udates are shipped over many channels that pilots should follow.