He had changed more mentally.

...he looked confused. No, that wasn't the right word, what he really looked like was torn, like he didn't know what to do. "How was your day?" Link asked him, innocently.

Zelda just stared off into space for a few seconds before coming up with an answer. "I don't know," he replied. His eyes met Link's, hesitently. "Link, am I a good person?"

A large part of Link wanted to snap at Zelda, to tell him that, in fact, he's been a **** and a cruel captor as of late. But she bit her tongue. She knew that the wiser course of action would be to sooth Zelda's ego, but gently admonish him too. "I still think you are," she told him. "But you haven't been acting like yourself. I want the old Zelda back, the one who cared about me, about other people."