She didn't. She's simply very perceptive.
She simply noticed that Cyril was visibly surprised/showed a reaction to seeing her even though it was supposedly the first time he had ever met her. (In this lifetime)
There's also a slight possibility she's knows about the current time Cyril (the one who is 5 years old) and could associate them both. Since the series hasn't shown the young Cyril from this timeline idk what happens if they both meet, or if they realize he's him.
She's just suspicious of him being a boy that is visibly someone who was raised a noble, having supposedly "shown up" at Arno with... Supposedly, no memories. If he has no memories why would he ever recognize her from somewhere else?
I don't know if I remember correctly but Eva also had past memories right?.. will she realize what's happening with cyril?