IIRC, that no contact order was put in place due to something that LE learned in the course of the investigation and forwarded it to the attention of CPS. Obviously CPS had already been involved in the case from the start, but IMO it seems that LE discovered or was notified about the info first. If true, it leads me to believe it was something learned in an interview or a tip. IMO, there's a good chance that SC threatened the boys into being quiet. Perhaps while LE was interviewing them, something slipped out and out of fear, whichever boy slipped, told LE that dad had threatened him. Either that or when they returned to school, still devastated and confused about their little sister's disappearance, mentioned something to a counselor or teacher about dad.
There needs to be a break in this case very soon. I would, as well as all you, love more than anything else, for this little girl to be found alive and unharmed.