I see "four boxes" was changed to "three boxes" in the remastered version, so that answers that!
Looks like there are still a few references to that fourth box, though. When they find the treasure at Arches,
Without being asked, Marina retrieves the screwdriver and hammer that I’ve been using to smash the locks. She sets them down in front of me, but I offer them to her.
But the Shiprock treasure wasn't locked. Was it originally written that they find treasure at Canyon de Chelly? This seems like a reference to a dig there:
Pangs of guilt remind me yet again of the broken brick at Canyon de Chelly, and I make my umpteenth resolution to be more careful.