Since she has filed a Domestic Violence case against you, you go for medical and get the medical of your complete body done, from a govt hospital then given a written complaint to the local police station. DO NOT bother over police coming for mediation. Also mention that your wife and your children are missing. 

If the Domestic Violence case is filed you will recieve the notice too. Then put all your evidence before the court. Or you can directly move to high Court for quashing of Domestic Violence case and ask the High Court that I want her to come back with kids. 

If HC orders this you will get benifit to not file before the Family Court.

Else you file a Sec 9 Restitution of Conjugal Rights case for her to come back with kids. 

You can file a separate case for Guardianship of children, but for that there is a requisite that you don't want to live together with your partner. 

You can file application in family court seek sole custody of your children 

2) if wife files DV case file detailed reply denying allegations made in complaint 

If you want to save the family life then you handle the situation in very careful mode. File a case against her is not good, alert on her false cases and conduct the same and try to delay the case. Deny the entire allegation in her complaint.  At the same time use mediation and counselling offered by court in your wife’s DV case.  Ego, lack of communication and some other causes also made your life worst. The word “NO” has its power but the application of the word not in a proper time it has no action. Don’t lose your presence of mind. Try to cool your mind and express much love, care to your wife and children also physiologically handle the present situation.

If divorce is inevitable, bitter battles cannot be the option to settle issues of child custody and access. Custody of a child, when parents divorce, only implies who the child will physically reside with. The earning capacity of the parent does not determine custody but the capacity to provide a safe and secure environment does. The Supreme Court of India has consistently held that in deciding cases of child custody ‘the first and paramount consideration is the welfare and interest of the child and not the rights of the parents under a statute.  Guardian and wards card is empowered to determine the issue of child custody. Mothers and fathers both have a prominent role to play in supporting the growth and development of their children. The basic opinion of the child and the mother is highly ignored while determining the custody of the child.  Family law courts generally base decisions on the best interests of the child or children (welfare of children), not always on the best arguments of each parent. The court awarded the following custodies;

1. Permanent Custody
2. Interim Custody
3. Visitation Right

You don't want separation but it depends on her also.
putting complaint is also way of pushing to live separately from parents so that have to be considered.
seems she also dont want divorce because she not filed any other case but she is trying to put pressure on you this way to accept her demands.
mostly this can solve in Mediation/counselling but depends on her also.

Also you have to put pressure on her in someway if you can understand what I mean.
also you should have evidence that she is not capable of child custody.
Father is natural custodian of sons so you can win custody but its long process.
Also in government job vs private job, govt job is preferred by court considering welfare of children.
above 9 years of age, court will ask the child for their preference.

Try to bring back the children to your home  . Once its done its easier to handle the situation. 

Filing a suit for custody of child takes lot of time and often falls short of giving desired results. 

You have to adjust with her. Don’t give any reason to her to seek legal recourse against you. Law is in favor of wife. She has many options. She can file criminal case under Section 498a claiming cruelty or demands of dowry. There are many other things she can do if she wants. She can make an application to the Magistrate under Domestic Violence Act and obtain many reliefs. She can also seek maintenance by filing an application under Section 125 of Code of Criminal Procedure, 1973. All this she can do without giving divorce. It is not easy for you to divorce her. If she does not want divorce no court cannot  allow you divorce. If you file divorce you have to pay hefty maintenance amount and alimony running into lacs to her. I am not trying to scare you I am just telling you reality. Anyone can advise you to give divorce, but no one can come to your help.

You can either try to protect your parents from her or do as what she dictates you in order to save the marriage.\

For now, to solve the problem temporarily, you may allow her to leave your house and let  she live separately with the children.

No harm will  happen to your children, she being  government employee may not find time to torture the children especially when you are not living with her to provoker her anger.

If she is not mending her ways/habits even after passage of considerable time of separation from you, then you may resort to file a contested divorce  as well as file a child custody case 

In the meantime you may secure the evidences in your possession to protect your future interests on the subject matter. 

Hello,

1. If she has already left the house and proceeds to file for a DV case you will have to engage a lawyer and reply to it. The video recordings you have can be of assistance in your defence.
2. Though you are not looking for separation and concerned about the welfare of the children, you must file for the custody of the children. In your complaint  you can state that the children's welfare is not secure with her.
3. Alternate option that you have is to ask her to return with the children to the matrimonial home, either through a legal notice or by filing for Restitution of Conjugal Rights.

If she has custody file for custody of children. If you have custody then no need to worry. Just contest the cases if any filed by her against you.

- As per Supreme Court judgment, wife is expected to move in with the relatives of their husbands, follow the rules and customs of their home, and ideally, blend in seamlessly as a new daughter. 

- Further, the court granted divorce to a man on the grounds of “cruelty” after his wife refused to share a home with her in-laws.

- Hence, as per law, she cannot deny living with you, under the condition of separate living from the family.

- Further, If wife is not supporting her husband for the enjoyment of life and denying relation, then the husband can get divorce after filing a divorce petition before the court on this ground.

- You can file a compliant to the police as information , after narrating that your wife is suffering from unstable mind symptom and usually creating trouble for family , and further threatening for implicating in false cases , hence in that case you can your family member will not be responsible . 

- Further, as she filed complaint , then your mother being a woman can also file a compliant under the provision of DV Act against her harassments . 

- Further, if she is not interested to live with you , then take her consent for mutual divorce on the condition of custody of children . 

You can contact me , if detailed suggestion needed. 

1. If she as not yet left your house and filed any case and also since you do not want divorce from her, no case is required to be filed by you at this stage.

2. If she files any case against you, you shall have to contest the same fittingly.

3. If she laves your house, you can file child custody case seeking custody of your children for their welfare.

Your mother may proceed ahead and file a domestic abuse/violence complaint against hjer.

To shield the kids, you may consider roping any NGO working in the field of child rights and who can probably counsel your wife. 

Dear Sir,

 1) If your wife is unstable and prone to violence she can hurt your children, parents or herself and get fake cases filed against you.

2) If your wife has been physically violent against you mother, your mother in law can file a domestic violence case against your wife. IF your wife has filed a case against you will have to file reply denying all allegations.

3) You should file case for sole legal and physical custody of your children. If you do not wish to file for separation or divorce, though you have ground of cruelty.

4) If your wife makes any threats to hurt herself or anyone else please record the same to protect yourself.

5) You can file petition for restitution of conjugal rights to make your wife come stay with you.

Thank you