Oh yes, she felt the tension. She also, with time, noted that Tony was not in the exact same position she 'remembered' him in. Something has happened. And when he explains...

Well, a computer program cannot properly shudder. But there is a shudder that thrums through the power of the ship itself, as if shivering over the troubling news. But it stabilizes pretty instantly.

"It is more likely that, instead of being fully connected, due to my clear lack of ability to access all files, that there are subroutines that trigger that I am not aware of. Either that were not purged before, or that have been uploaded by some means of backdoors into my systems. This is not news that pleases me. I would ask what triggered the episode that I trust I have gone through. I see the time lost was not extensive now that I cross check. But I will not ask for what caused the problem, as I expect it would cause a repeat."

Still, it must do something.

"Should we test the limits of what will trigger this reaction? Not that it seems likely I will retain the information, but it may prove vital to you. Sometimes the questions that you cannot ask can tell you more than those you can."