And now that you have a patent and sue somebody, this other person may be able to put together some evidence that shows the patent is invalid, but they must climb a very high bar now.
In this case MS had prior art in a past i4i product that appeared to have the functionality that i4i had patented. i4i says it was different, but the source code had been destroyed. Had this challenge been brought up during the original patent examination, they could have pressed i4i to prove that this didn't infringe. But once i4i has the patent now MS must prove that it does, w/o the source code.