"Although I don't understand all the dynamics here, Hinduism seems to have had a serious resurgence under Moslem rule. Possibly this had something to do with Mongol religious politics ~ they had just been in some serious wars with Buddhism for several centuries. Others with a better command of Indian and Mongolian history could probably address the question"
India was a Buddhist country till about 600 - 700 AD when it was re-converted to "Hinduism" by Sri Sankracharya. It had about 400 years of renewed glory before the Islamic onslaught. It was in wane from 1100 AD till 1990 when the RSS/BJP came to power.
Conflict was inevitable.
No wonder all those Jain and Buddhist Temples have been been overbuilt with Hindu temples and Moslem mosques.