Did I miss something?

I don't remember seeing Sidney find out that Vaughn is still alive... has she always known? Did they cover that part and I completely missed it? Are they going to do a flashback of her finding out he is alive or something?? I am so confused!
 
I think the implication is that Sydney always knew Vaughn was alive, she jsut had to pretend he was dead so Prophet 5 wouldn't try to kill him again.
 
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