Do you mean at the time of the article by Novak?
We know she was undercover when she started because it was revealed that she was a Career Trainee--all Career Trainees are undercover and typically will be undercover throughout their careers, no matter what job they have. Also, all employees stationed overseas are undercover.
If she became an open employee some time between coming back to the states and the Novak article being written, that's possible. I tend to doubt it--anyone could take one look at her file and see that she was an open employee and that would be the end of it. There's no voodoo in determining your status--you are or you aren't.
I just don't see how any of this could have proceeded past the first minute of the first accusation if she wasn't undercover--that's something the administration could determine with a phone call. In addition, all of her coworkers would know one way or the other if she was open or covert. If she turns out not to be an undercover employee, there's something seriously wrong with this prosecutor, this administration, the Justice Department and anyone else involved--it shouldn't take two years and millions of dollars just to find out she wasn't undercover. There's just no way.