Doubts of mutual divorce

To me, she is ready to give you a divorce and if you also want to give divorce then both of you jointly apply for divorce.  If your wife prays the court for maintenance given by the court, she may be granted maintenance depend on the income of you both.

Firstly, the information provided is insufficient as you have not written whether you want a divorce or not. If you are not ready then she cannot file a divorce petition under mutual consent. ( Reference- Section 13B of Hindu Marriage Act 1955).
Secondly, If she is filing for a divorce individually then it depends upon the reason why your wife left your house and started living with her parents for 6 years which you have mentioned that it was a misunderstanding. ( Section 13(1) of Hindu Marriage Act 1955) 
Finally (Your Main Concern), you have not mentioned your wife's income. If she proves that she will not be able support herself with her current earnings, the judge might order you pay alimony to your wife (Reference- Section 25(1) of Hindu Marriage Act 1955). She cannot claim a part of your ancestral property as she has not contributed anything to buy it but she has a right to ask for alimony as I have mentioned earlier.

If both of you are willing and ready to get a decree of divorce by mutual consent, you will have to move a petition accordingly wherein you will have to pay alimony for her life even if she is earning more than you, as agreed between both of you.

Consult and engage a local prudent lawyer for appreciation of facts, professional advise and necessary proceeding.

Yes, a common petition needs to be filed. Terms of divorce would be as mutually agreed.  Generally, the decree of divorce is granted after a cooling time, once the joint petition is filed.