She doesn't notice how much things have really changed until Nick walks back in those doors. It's not the new waddle to her walk or the tan peaking out from his collar, but there is something new in the air around them. Maybe it's a result of watching Carisi with the new "new guy", feeling guilty for how she treated him as a rookie, or maybe it's the now established bond between herself and the tall blonde, but when Nick makes a crack at Carisi's expense she feels something akin to anger. She attempts a half-hearted smile his way and bites her tongue. And that night she lays awake and plays through all the times she tore down Carisi, and all the times he still bothered to build her up.
Then one day he makes the self-deprecating comment of "guess I'm still that 'work in progress' hey" and she can recall just how devastated his eyes had been when she referred to him like that. So she tries to make amends by calling his attention and offering a "No, Carisi, you're… you're… good." It's lame and unbelievably awkward but the boy's eyes light up and he smiles at her with a rough thank you. She waits til he walks away before throwing her pen at the chuckling Finn watching from the coffee pot.