SHOPIAN, Kashmir  The case had all the hallmarks of a grisly and politically explosive crime, and it plunged the volatile Kashmir Valley into months of violent protests and political turmoil. Two young women were found dead in May in a stream flanked by military and police camps, and doctors who performed autopsies said that they had been raped and murdered.

But evidence from a new and more complete pair of autopsies and three months of intensive investigation by India’s top police agency have added surprising power to arguments that the women did in fact drown, as the Kashmiri authorities initially announced, in a normally placid stream swollen dangerously with glacial runoff.

The initial charges of rape and murder fueled rage at the hundreds of thousands of security forces whom India deploys here in what many Kashmiris see as an occupation. Four members of the Kashmiri police force, which works closely with the Indian authorities, were arrested.

Ratn Sanjay, who led the Central Bureau of Investigation’s inquiry into the deaths, said that when his team began its work in September at the request of the state government, the assumption was that the women had been raped and murdered. But that eroded rapidly as investigators discovered discrepancies between several autopsy reports prepared the day the women’s bodies were found, including mislabeled tissue.