Seriously I feel bad for JonBenét but there's nothing normal people could do about it, The Case is closed
I mean, there's no harm in speculating.
I think John Ramsey was regularly molesting his daughter. He would do it at night, after Patsy would go to bed, and he would bring her somewhere private, like the wine cellar. Although there was no evidence of ****, there was evidence her vaginal area could have been contaminated by the paint brush/rod and what not, wherein the killer then wiped her with a cloth. This is only something a person who had been regularly abusing her would do. The killer also changed her clothes for her from what Patsy changed her in before they went to bed, which means the killer was in her room, had access to her clothes, and generally, simply had access to her. I think that she may have reacted badly to the abuse and John tried to silence her and accidentally killed her.