What's that got to do with the derelict? Bishop mentioned "the size of Nebraska", but you have to factor in how the Jordans apparently took two whole weeks to reach the derelict. So long as someone comes up with a reason for why the company did not make an expedition to the derelict, in the intervening years between the third and fourth films, it could well be there. Such a reason could be that perhaps the stuff on the surface got destroyed, but the silo cave, below ground, still remained intact.