What are the consequences of mutual divorce on the ongoing cases?

My son was married in Nov'15. Marries did consumate. she left for her paternal home within a week & did not come My son filed judicial separation U/s 10 HM act. After that she filed case U/s 498a & DV against 4 members of our family. we obtained stay from Hon. High court. Stay was granted as the JS case was pending in family court. Recently on the initiative of family court conselling was done and and we agreed for mutual divorce on some fixed alimony payable in 4 installments.Both of us agreed to withdraw all cases. Based on mediation agreement we paid first installment of alimony and joint mutual divorce petition was submitted in court. Now my query is -- 1) Since the stay on 498a and DV was granted on the basis of pending case of judicial separation in lower court, is it so that it will be deemed to be vacated automatically once the pending judicial separation case U/s 10 of HM act is converted into divorce case.