When you enter Gehennom, the Sanctum is right there as one of the first couple of levels. But entering it transforms all the existing dungeon levels irreversibly into Gehennom levels, including demon lord lairs and the like. Everything in the Dungeons of Doom will be lost, and the player now has to work their way through the rest of Gehennom with the Amulet to enter the Planes.

Alternatively, and perhaps more straightforwardly, destroy the Dungeons of Doom when the player goes beneath the Valley of the Dead, and just have them enter the Planes directly from the Sanctum.