Brahmin missionaries from the north (mainly from Saurastra and Konkan region) in 800AD through Tulu-Nadu (Mangalore area). At that point in time, Kerala was a flourishing center for Buddhism and Jainism. They were successful in converting the local Chera kings. This led to a more systematic settlement of 64 gramams and Illoms across Kerala.
The Tamil 'Aalavaipathikam' records that around 640 A.D., Sambanda Murti, a Brahmin, won over the Pandya royal family and caused the massacre of 8,000 Buddhist monks in Madurai; Buddhist nuns were reportedly made into devadasis and relocated in the Hindu temple precincts. The persecution and eventual exodus of Buddhists from Tamil Nadu to Kerala in the seventh century was occasioned by the fall of the Buddhist Kalabhras at the hands of the Pandyas.
If this is what happened in the neighboring Tamil kingdoms then imagine what must have happened in our Kerala. It's a mystery that is not solved. Most of the history have been rewritten by the Brahmins, the so called theory of defeating Buddhist scholars in debate and brought Hinduism back in India story created by them.