The other party has ran away with your son and not allowing you even the ordered visitation and your stupid lawyer telling you cannot seek the custody of the child as there was an agreement. Change your lawyer.
The custody order cannot be permanent by any means and with change of circumstance it can be altered, tell this to your stupid lawyer. What if your ex-wife dies, who will have your son's custody in that case, will the son also go with your wife as you had agreed for it? This what the standard of Tis Hazari lawyers.
You can always seek fresh order for child custody from court if the previous order was disobeyed by the other party.
As far filing Writ of Habeas Corpus in Delhi High Court that can be another option for you but here again the very first question put by the bench hearing the Writ Petition why the custody not claimed from the district court before coming to High Court. Yes you can always tell about the wife absconding with your son and Delhi Police being made first party in Writ will be directed to produce the child in the court if the Writ gets admitted.
As far issuing arrest warrant in Civil Case is concerned that is very much possible if you file Criminal Contempt against your wife, who has by disobeying the agreement which became part of court order and purposely avoiding appearance in court.