How do I help my son and granddaughter?

My 21 year old son just got custody of his 18 month old daughter 2 months ago and found out about her existence 4 months ago when her mother died and her boyfriend was imprisoned for her death and physically abusing her and the baby. He found out through her friends that he was the father but that she was afraid of her boyfriend so she never told my son, but he just knew it was his baby since she looks identical to his baby pictures. He had a lot of court issues since the ex was on the birth certificate but that's all cleared up now, but my granddaughter has showed extreme emotional issues. She's extremely clingy towards my son and if he leaves for a second, but gets really really upset. He just started going back to school 2 weeks ago so me and my husband watch her and its been hell. She won't sleep alone and if my son so much as raises his voice, she runs around screaming like she's in pain. One time my son had a belt in his hand (he was putting it on, not discipling her) but when she saw it she ran away from him and hid for 2 hours. When he found her, she was in absolute terror and had dug her nails into her arms. It was horrible. Her "step-father" used to beat her mother in front her her so she gets scared when she hears people arguing, and they used to leave her alone for hours on end, which explains the separation anxiety. My son loves her very much, (as do all of us) but we're not sure how to help her.