The Jonang were suppressed in central Tibet in the seventeenth century, and what survived did so because the suppression was incomplete in ways the suppressors did not record.
The teaching that caused it
Dolpopa held that emptiness is of two kinds: phenomena are empty of themselves, but the ultimate is empty only of what is other than it, and is itself replete. Every other Tibetan school reads emptiness as self-emptiness throughout and treats the Jonang position as a form of eternalism. Dolpopa took his position to be the plain sense of the tantras and of the buddha-nature literature, not an innovation.
Why Kalachakra
The Kalachakra tantra is the Jonang's special transmission, and the school preserved the fullest Tibetan commentarial tradition on it and on its six-branch yoga. That transmission is the reason the school's material stayed in circulation: other schools continued to receive Kalachakra teaching from Jonang lineage holders even while rejecting the philosophy attached to it. Taranatha, the last great figure before the suppression, is still read across the traditions as a historian.
Survival in the east
Monasteries were converted and printing blocks were sealed in the central provinces, but Jonang communities in Amdo and Golok in the far east were never absorbed, and have continued unbroken to the present. They were not officially recognised as a distinct school again until the twenty-first century, having been counted for three hundred years as something that had ended.