The Jonang School was thought to be extinguished during the time of the 5th Dalai Lama, as the 5th Dalai Lama wanted to suppress this school who were supporters of the rivals to the 5th Dalai Lama. Civil war broke out in Tibet. Historians also came to the conclusion that the Jonang was suppressed not so much of that they were heretical, but it was purely due to politics as the Great 5th needed to bring stability to the country once again after the civil war. The Gelug school also embraced the Jonang tradition of Kalachkara, and Kalachakara is being propitiated by the Dalai Lama up to now.
In recent times it had been discovered that Jonang Monasteries are still active in Sichuan, China areas.
The 14th Dalai Lama confirmed this view in Glenn Mullin's The Fourteen Dalai Lamas (Clear Light Publishers, p. 207):
"These monasteries were closed for political reasons, not religious ones, and their closing had nothing to do with sectarianism. They had supported the Tsangpa king in the uprising, thus committing treason. The Great Fifth believed that they should be closed in order to insure the future stability of the (Tibetan) nation, and to dissuade other monasteries from engaging in warfare."
Rediscovery - From Wikipedia
The Jonangpa were until recently thought to be an extinct heretical sect. Thus, Tibetologists were astonished when fieldwork turned up several active Jonangpa monasteries, including the main monastery called Tsangwa located in Tibet, Dzamthang County, Sichuan, China. Almost 40 monasteries, comprising about 5,000 monks, have subsequently been found, including some in the Amdo and Gyarong districts of Qinghai and the Tibet Autonomous Region.[2]
Interestingly, one of the primary supporters of the Jonang lineage in exile has been the 14th Dalai Lama of the Gelugpa. The Dalai Lama donated buildings in Himachal Pradesh state in Shimla, India for use as a Jonang monastery (now known as the Main Takten Phuntsok Choeling Monastery) and has visited during one of his recent teaching tours. The Karmapa of the Karma Kagyu lineage has visited there as well.
The Jonang tradition has recently officially registered with the Tibetan Government in exile to be recognized as the fifth living Buddhist tradition of Tibet. The 14th Dalai Lama assigned Khalkha Jetsun Dampa Rinpoche or the 'Bogd Gegeen' of Mongolia (who is considered to be an incarnation of Taranatha) as the leader of the Jonang tradition.
So if the 14th Dalai Lama could reverse what the 5th Dalai Lama he can surely reverse his stance on the ban. Stay tuned, this forum and website has the coolest news on the lifting of the ban!