You would have ethnic cleansing. Simple as that.
A distinction should be made between a violent collapse of the Raj and the most violent scenario which would be the full on balkanization of India. In either case the Muslims can't make Hindu majority areas Muslim though they can overthrow Hindu leaders in places like Kashmir. Neither can the Hindus wipe the Muslims out, though you might see a few million Muslims dead in the worst case scenarios and many more millions dead if the balkanization of India happens.
Even in violent collapse (again not the most violent because that leads to balkanization and Hindus fighting Hindus) of the Raj I do not think the Hindus would be seeking to wipe out the Muslims, just marginalize them. There would be no attempt to turn OTL Bangladesh or Sindh Hindu for example, they can stay Muslim. What will happen will be the destruction of the Muslim League and the idea of Pakistan. All Muslim territories would become Indian States answerable to the Indian Congress.
The exception to this would be the Punjab. From a nationalists point of view the demographics there could be "tweaked" so that instead of there being a Muslim majority, there would be Hindu/Sikh plurality. Without the Punjab the idea of Pakistan is dead and that region would undoubtedly see the most bloodshed with possibly millions of deaths from ethnic cleansing.