First I just want to say, something else happened while you were gone.
I have nine birds as you know and two kids, a cat, a dog, a guinea pig, hermit crabs, and a betta fish. I'm ALWAYS yelling at someone. Including my birds if they're being TOO noisy. Nothing mean, just "hey, mommy's trying to finish a paper!" and they'll look at me as though saying, "and?...."
That being said, I think her fear has more to do with yelling. My birds do not cower from my hands ever. Even when I'm yelling. Animals, like children or people, only cower from a hand when they've been struck or threatened with a strike.
I think more has happened and that is not good or healthy for that bird. You need to find out before it's too late.