They may have officially transferred the plane, but do you really think that means the CIA would have to stop operating it? I mean it is totally possible that they did, but I could see an equally possible scenario where they just "transfered" it for political cover.
Since the DOJ has been using it for all sorts of non-Snowden business (Google will show you this quickly), I'm not sure where this logic gets you; the same logic suggests any US plane could be a secret CIA plane. That's true, they all could. And?