Emma’s big fears with Neal seem to center around fear of not being loved (she’s coming to terms with Neal really having loved her) and fear of losing him/not being with him. With time, and the assurances of Neal’s ongoing presence in her life no matter what, those fears seem managable.
I think this is really important. Her whole life, Emma has felt unloved and unwanted. And when Neal left, she thought it was because he didn’t really love her and that was devastating. But now she is realizing that he has always loved her (just like she has always loved him) and I think, more importantly, Emma might soon start to realize just how manipulated her whole life has been. The events of the past arent what they were thought to be.