The array didn't stop working because of the updates that removed Linux. The Air Force is using the PS3s for their computing power, which is built in, not the games, features and menu interfaces that Sony's updates typically address. So the Air Force didn't run the updates, because its PS3s aren't used for gaming or signing in to the PlayStation Network. The problem, though, is that when a machine needs to be replaced, the Air Force will no longer be able to readily get a Linux-capable PS3.

http://arstechnica.com/gaming/news/2010/05/how-removing-ps3-linux-hurts-the-air-force.ars