Oh, Barnabas had figured out that Julia "cared" for him quite some time before that scene with Carolyn during the "let's scare Julia out of her mind" storyline.
Before she began the final phase of the 1967 "experiment," Julia told Barnabas that "there might be someone who would accept you and love you as you are now." In a voice dripping with sarcasm, Barnabas stated that he'd like to meet such a woman! He clearly realized that Jules was talking about herself.
This is around the same time when Barnabas addresses Julia as "my dear" whenever he's trying to manipulate her. He is a lot nicer to her in the 1968 storyline. In 1967 you get the feeling that he did not fully appreciate how much she cared for him until she had offered her own throat to "cure" him from his disastrous aging. "Why, Julia?" he asks in a way that suggests he feels briefly humbled by such self-sacrifice.
In the current storyline (1968 ) he does come to realize how much HE cares about HER in a later plot development ...
Gothick