John Doe 1 and John Doe 2? In theory they didn't know who they were.
On the other hand I just read an article where they were admitting to interviewing him for a foreign government in the past. And, if you believe his mom they were essentially following his every move. With that in mind he must have been in the FBI database one way or another. So, I do wonder about that.
If he lives then they will have to show their evidence. Well, unless he pleads guilty. Maybe a plea for spilling the beans on others. Anything could happen!