498a/406 discharge, post mutual divorce. cri. case yet to frame charges

The divorce case is a different subject to that of the pending criminal cases under sections 498a and 406 IPC etc., 

The criminal cases will not be automatically discharged on divorce on the grounds of mutual consent.

You may have to approach high court with a petition under section 482 cr.p.c. seeking to quash the same on the basis of mutual consent divorce already granted by the family court by attaching a copy of the divorce decree. 

It would be more proper if she files an affidavit expressing her no objection to the quash petition by appearing in person before high court.

1. Yes. It wont be automatically discharged. but can I submit a fresh discharge application with a copy of MCD?

2. I dont expect her to make any effort for me. She will just ask for more money. (and ask for more at the last moment. She has done it before.)

In the pending discharge petition itself you can file a petition to receive additional documents, and the additional document would be the certified  copy of the mutual consent divorce decree, hence there may not be a necessity to file a fresh discharge petition. The court will not entertain any fresh discharge petition based on the subsequent developments, hence at the time of arguments also you can add this information about the divorce happened between you both.

However you must bear it in mind that the discharge petition was originally filed based on the circumstances that prevailed at that time of filing the petition and not based on the subsequent development, hence you better go for quash petition by attaching the copy of the divorce decree to convince the high court about your present situation and seek the desired relief.

If nothing comes to your rescue, then you may better challenge the false case in the trial court itself and get acquitted based on the developments that took place subsequently 

You will have to get the FIR quashed, if already registered.

criminal allegations arising out of marraige do not extinguish with the divorce.

We have now converted the divorce into MCD. firt motion done. its mentioned that she will cooperate to end the criminal cases on family. Plan is to appear on next date and move forward with Frame of Charge, her witness in front of judge (where she will deny) and close the matter. and finish MCD after that.

The issue - one of the accused (Accused 3) has never been and never will be present in the court.  Ergo, there is no vakaltnama from A3 either. However other accused are present and will be in court.

How does this proceed. Will all 3 accused get acquitted?   

Trial will commence or framing will commence only in the presence of all the accused persons. Otherwise the policde have to file a petition to split the accused and proceed with the available accused persons and the complainant should turn hostile.