Lexi used to hide under the bed from my son. He was fine with it and didn't really bother her much. One day he called me and told me her hair clip popped when he picked her up. My baby would NEVER allow him (or anyone else for that matter) to pick her up. When I got home, sure enough, she ran to him, jumped up on his legs and waited for him to pick her, smiling and wagging her tail. I was flabbergasted. She won't even let ME pick her up without trickery.
I don't know when she changed her mind, but she absolutely adores him, and he adores her. Give her time, I'll bet she'll come around.