Tommaso Previato : Mongol schism and conversion
"After a short period ... in which Islam was temporarily displaced from its position as state religion and the Mongols still remained torn between Buddhist-Nestorian beliefs of the Turkic-Uyghur tradition and the Arabo-Persian ones, the attendants of the house of Chaghatay (1183–1242), forced to find new ways of ruling over the heterogeneous Muslim population, began to support local Sufism seeing in it an effective tool to legitimate their governance and gain authority from the traditional institutions of local Muslim elites. It was at the dawn of the fourteenth century, that they came into contact with local Sufis and decided to convert to Islam, seemingly because driven by the will to follow the example of Chagathay’s younger brother Ögedey (1186–1241) grand Khan, who was more sympathetically inclined towards the Muslims"
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This prolonged chain of conversions concomitantly triggered an anti-Muslim reaction among some conservative members of the royal family, which manifested continuing adherence to the great yasa (lit. ordinance), the costomary law of the steppe as codified by Genghis. It was clear that unity could no longer be ensured. The ideological schism that followed, in the middle fourteenth century, broke the khanate in two: the eastern half known as Moghulistan, based in Almalik (in the Yili 伊 犁 river valley, northern Xinjiang), largely retaining the normative practices and beliefs of their ancestors into the framework of a nomad state; and the western one in Transoxania, which endeavoured to combine the zeal of Persian-Islamic culture with the traditional Mongol heritage but in the long run could not keep from implementing the shari’a. It was exactly under these circumstances that the newly-formed Naqshbandiyya 納格什班底耶 Sufi order, by placing utmost emphasis on social and political aspects of religious life, stepped into the breach and turned itself into an effective tool against the Moghul’s 'infide' governance. Since Baha-ud-Din Naqshband Bukhari 伊本·白哈 丁 (1318–1389) established the order around Bukhara, the Naqshbandiyya shortly became the dominant Sufi organization in Central Asia and the Chinese Turkestan (nowadays Xinjiang). Its teachings proved suitable enough for the Mongol ruling class of the western khanate, who only one century after Chaghatay’s death definitely lose power to the Timurids (1370–1507). Initiator of a brand-new, fully Perso-Islamic dynasty yet stemming from the noblest Turko-Mongol lineage, the great Timur/Tamerlane 帖木兒 (r. 1370–1405) was himself a Naqshbandiyya follower that paid Sufi sheikhs particular honor. Such a profound change could not have been achieved solely during his rule, it must undoubtedly be the completion of a long acculturation process that had started at least three generations before, with Tarmashirin seizing the throne.
What remains indisputable is that the first contact the Chaghatayid had with the Sufis and Islamic culture at large was by no means congenial. Differently from the other ulus which essentially were peopled by agriculturalists, the Chagatay Kingdom was highly diversified as pertains to lifestyles and ethnic-religious composition, hence the Sufis at first might have exerted some sort of influence merely to certain segments of society, and the pastoral-nomads were surely not parting with them.
A letter written by the Sufi Sayf al-Din al-Bakharzi (1190–1261) to the Kutb al-Din Habash ‘Amid, the regent-vizier of Chaghatay, the Muslim elites were initially deeply disappointed about the Mongol rulership and tried in several occasions to push the Khan’s royal family in favour of Sufism.
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The first to establish one of the most influential sects based on the Naqshbandi’s knowledge set was Ma Laichi 馬来遲 (1681?–1766). After coming back from Haji Islamic Networks under the Mongol Rule 249 and having spent almost five years abroad (in Middle East and Central Asia, namely Mecca, Yemen and Bukhara) to study the Qur’an, Ma Laichi made himself the founder of the “Flower Mosque” brotherhood (花寺門宦) of the Khufiyyah order (虎夫耶, later named “Old Teachings” 老教). While, his fellow student Ma Mingxin 馬明心 (1719–1781) held different opinions that led him to initiate a revised version of Sufism, known under the name of Jahriyyah (哲赫林耶, also called “New Teachings” 新教). ...
This split triggered a series of internal struggles, that attracted the attention of the highest Court in Gansu. The Qing authorities decided in favor of the Kufiyyah, presumably because it was the oldest between the two congregations. Ma Mingxin was then arrested and put to death, together with his disciple the Salar commander Susishisan (1729–1781) who died soon afterwards in the effort to seek revenge.
Conclusion: normalization of state - Muslims relations "had sectarian differences institutionalized, along with a highly ideological and polarized dichotomy 'bad Muslim 回匪-good Muslim良回' which ultimately come on the scene with inevitable consequences for all Sufi tariqahs."