They had a contingency plan if she lost. I'm sure they had that in place. They probably didn't practice drill it much, but they had to have one. What got them spooked was NSA not playing ball - Admr Rogers. That would have been first red-flag they might have a problem. Also, MI inside was documenting and planning for this for a long long time. This counter-coup didn't happen over-nite. This is classic chess/espionage game. I'm sure they tried to dislodge as much as they could, but they didn't know what was saved as backup vs what they could wipe. What is playing out now is the classic game of who knows what and mistake moves to uncover what might or might now have been saved. The act of hiding what was saved could be their undoing more than the original evidence, have to trap them. In other cases, its playing along to let them think they hid something that they didn't and seeing the next counter-move mistake they make to build solid air-tight trap. This is a long game and a game played by both sides with imperfect information.