Could my nephew have been ually abused?

My nephew is 2 years old. Up until a month ago, he was living with his mother and her live-in boyfriend, who I will just call Tom here. Tom (the boyfriend) was verbally, emotionally, & physically abusive to my sister, which she finally admitted to me very recently. She also admitted that Tom hit my nephew so hard on his legs that it left welts. He would him for no reason. My sister didn't stop her boyfriend from hitting her child. My nephew is now living with me and my mother, but my worry has not dissipated. Although I am his aunt, he calls me "momma" often and his behavior has changed drastically. For instance, he is terrified to be put into bed at night. He does anything to stay out of bed & stay with us. He will scream for hours straight, his voice raw, if we don't get him. He was never like this before. He used to lay down with no problem. Nap time isn’t really a problem. The problem is only at night time- bedtime. He also has grabbed his & and messed with it a few times. I can not say if this is normal boy curiosity, or more? He doesn’t seem to be masturbating, but has called his “a hole”. He knows you put things into holes- like blocks into a toy with appropriately shaped holes. His attitude has worsened. He gets angry easily, has bouts of rage. I know he is 2 and the developmental stage he has reached outlines this defiance & autonomy as normal patterns of behavior, but he was never this volatile in the past. He never slapped in the face, or threw things, or ran away from us, spouting curse words that we had no idea he even knew. I also noted a couple of months ago, when he was still living with his mother & Tom, that after staying with me for the weekend, he was terrified to go back to his mother. He clutched to me & seemed afraid of his mother & Tom. He was clearly terrified, panicked, to go with his own mother. He screamed 'NO!" & curled his fingers into me. My sister had to forcefully take him from my arms. He has nightmares. We've noticed that he suddenly developed awful nightmares where he thrashes wildly in bed screaming, "NO! NO!". It's greatly disturbing to see him gripped by that kind of fear. So, because I don't think there’d be any physical trauma anymore, & my sister & Tom will admit nothing I need to know if my fears are valid. I don't want to put my nephew through something like therapy or a medical examination for nothing, but I fear the day my sister comes to get her son again. Will the abuse start again? I have no legal rights to keep him from her, even though I have filed a report with the local police department & called DHR. They say I can’t do anything, that my hands are tied if I want temporary or full custody. But if I could somehow get some kind of emotional/psychological proof of his abuse then I might be able to ensure his safety after all. What should I do? Should I go with my gut feeling that he IS being abused & seek help? If so, who should I go to with my concerns...?