You shall file compromise petition in the court. After compromise decree issued by the court you can execute release deed to and register it in SRO concerned.
The proper course is filing a petition before the competent court for referring the same to Lokpal /Legal Services Authority and bringing compromise deed the status of award, and sending the deed through LSA to Registrar. The parties are entitled for return of court fee also and this is the proper way to settle the disputes among the parties in litigation.