The cellphones wouldn't have been destroyed at all. What "software" are you people thinking of? The signal is the same signal your phone uses for phone calls, text messages. Where the signal is sent from and received, that area is mapped by Bruce's machine. Thousands off cell phone activity going on in Gotham at every given moment makes it one giant radar. Destroying the machine that picks up those frequencies wouldn't destroy the cell phones o_o. That's like almost saying blowing up the internet would fry my computer.