How can NRI couple married in India get mutual divorce? Where to file?

With respect to matrimonial disputes, the jurisdiction of courts is determined based on the following considerations:

i. Where the marriage was solemnized
ii. Where the couple last stayed together (the matrimonial home)

In your nephew’s case, they are amenable to the jurisdiction of both India and US. So, they can file a divorce petition either in India or in USA. 

However, we would like to mention that it is preferred that you file the divorce petition in India as a divorce decree passed in USA can be challenged and declared null and void in India on the following grounds:

i. When Granted by Court not authorised by Indian Law to grant the same
ii. When one side is not heard or his/her submissions not taken on record
iii. On a ground not recognised by Indian Law
iv. When the proceedings are against principles of Natural Justice
v. If it is obtained by fraud

In such a case you shall end up divorced in USA and married in India. 

2. As a marriage registered in India is recognized in USA, similarly a divorce decree passed in India is also recognized in USA. India is the court of competent jurisdiction as the marriage was solemnized in India as per Hindu rites and rituals under the Hindu Marriage Act and even registered in India.

3. After a divorce decree is passed in India, you shall have to file a case for recognition of the said decree in USA and your divorce shall be recognized in USA. 

4. Yes the divorce proceedings for mutual consent divorce can be initiated in India through video conferencing by sending over a Power of Attorney. 

5. The Court under Mutual Consent Divorce gives a statutory period of 6 months for the parties to resolve the dispute and in case the parties are unable to resolve their issues within this time period, the divorce is granted.