Interesting that Mr. Galloway never thought to back up his system, leaving a copy in an obscure cabinet we it wouldn't also have been destroyed. Of course, carrying a copy out would have violated all kinds of trade secret laws...
As to the "patented == public", the key word there is details. I may be able to patent a device that levitates a battleship with only a 9V battery as a power source--the details of how that's done (electronic circuits, rare earth compounds, how coils are wound, naquadah reactor, etc) do _not_ have to be disclosed, and can remain trade secrets. That's what the NDA applies to.