There are many states in India where Hindus are in minority but still deprived of getting minority special status.
Jammu & Kashmir
After a continuous struggle of six centuries and several failed attempts of Umayyads, Abbasids, Ghaznavids, Kashmir finally fell into Muslim hands in mid of 14th century CE.Because of severe atrocities like forceful mass conversion, destructions of temples, abduction of women and massacres Hindus became minority in the region. In 1990 there were around 5 lakh Kashmiri Hindus who were compelled to leave the valley by Pakistan sponsored terrorism.
Today, there are only 28.34% (2011 census) Hindus in Jammu and Kashmir, completely wiped out from POK and Kashmir valley.
The ancient Panchnad region of Vedic Hindus faced countless invasion even since Alexander and before. But kept standing proudly as the bulwark of Bharat.
The Muslim atrocities medieval era reduced Hindu population to great extent. In 1947, a larger part of Punjab went into Pakistan where Hindus and Hindudom has been completely wiped out.
Today in Indian Punjab the Hindu population is only 38.5%.
Until the beginning of 19th century, the total population of Meghalaya was following indigenous religion. Ceaseless conversion for last two centuries has made the sate 75% Christian.
Today, Hindu population in Meghalaya is 11% only.
Arunachal Pradesh is the region where sage Parashuram washed away sins, the sage Vyasa meditated, King Bhishmaka founded his kingdom, and Lord Krishna married his consort Rukmini.
Today, Hindu population is only 29% in Arunachal Pradesh
Until the beginning of 18th century, 100% Manipuris were following indigenous religion.
Today Hindu population in Manipur is only 41%
Till early 19th century, Naga people were followers of indigenous religion.
Today, Hindu Population is only 8%.
In union territory of Lakshdweep the Hindu Population is only 2%.
Source: Census 2011.