As per the offence under section 363, the consent of the lawful gurdian is necessary but it is clear from the facts narrated by you that no act took place by your nephew which can be construed as "taking or enticing" hence the ingridents neccessary to make out the offence does not get satisfied.
Normally, in cases like these Police produce the girl before the Magistrate for recording of her statement u/s 164 Cr.P.C. If the statement is in the favor of your nephew then court will surely take notice of that. If such a statement is not recorded, then the girl will be produced before the Magistrate, trying the case, where she will have to depose in favor of your nephew.
You can also approach the High Court U/s 482 Cr.P.C for quashing of charge sheet (Final report) and FIR and there you can get the notice issued to the girl who will depose in your favor, which hopefully will end your trauma.