In the event that any of the designations set forth in this chapter or a shoreline master program approved under WAC 173-18-044, conflict with the criteria set forth in RCW 90.58.030(2) or in WAC 173-18-040 the criteria shall control. The designation of the stream or river shall be governed by the criteria, except that the local government must amend the local master program to reflect the new designation within three years of the discovery of the discrepancy.