What to do if brother's wife accuse family of false dowry case?

See if the wife is not happy in the relationship and has already been living separately since August 2013, then you should probably speak to her if she is willing to get a divorce and both your brother and his wife can file a petition for divorce by mutual consent. 

Prior to that you can enter into a settlement agreement on the distribution of assets, maintenance, alimony etc.

If she is not willing to go for a divorce, then firstly intimate the police by way of a written intimation that you suspect that she is going to file false case against you. Collect evidence to prove that no dowry was demanded and no incidence of domestic violence ever took place.

Thereafter, your brother can file a petition for divorce on the grounds of mental cruelty under Section 13(1) of the Hindu Marriage Act. This can be easily proven by the fact that she left her matrimonial home leaving behind her daughter and old in-laws.