Some scholars assume that in 1450 in the church of St. Sophia, a council was summoned which was attended by numerous representatives of the Orthodox clergy who had come to Constantinople, among them the patriarchs of Antioch, Alexandria, and Jerusalem; this council condemned the union and its partisans and announced the restoration of Orthodoxy. Leo Allatius, a very well-known scholar in Italy in the seventeenth century, was the first to publish the fragments of the acts of this council but he considered them spurious. Since then the opinions of scholars have been divided: some, following the example of Allatius, regarded the acts of the council as spurious and affirmed that the council itself never existed; others, Greek theologians and Greek scholars in particular, who were exceedingly interested in such a council, considered the published acts genuine and the convocation of the Council of St. Sophia a historical fact. In more recent times, the tendency has been to consider the acts of the Council of St. Sophia false and to deny the very fact of the convocation of the council, although some scholars still aver that the council really took place. There is not enough evidence to affirm that under Constantine there was an open break from the union confirmed by a council. On the contrary, when he saw fatal danger approaching the city, Constantine again appealed for aid to the West. Instead of the desired military aid, only the former metropolitan of Moscow, Isidore, who had participated in the Union of Florence, now a cardinal in the Roman Catholic church, arrived in Constantinople and in December 1452, five months before the fall of the city, read in St. Sophia the solemn promulgation of union and celebrated the union liturgy, including the name of the pope. This act at such a crisis aroused the greatest agitation among the population of the city.
After the fall of Constantinople, the religion and religious institutions of the Greeks were preserved under the Turkish sway. In spite of the occasional violence of the Turkish government and the Muhammedan people against the representatives of the Greek church and the Orthodox population, under Muhammed II and his immediate successors the religious rights which had been granted the Christians were strictly observed. The patriarch, bishops, and priests were proclaimed inviolable. The clergy was exempted from taxes, while all the rest of the Greeks were obliged to pay an annual tribute (charadj). Half of the churches in the capital were converted into mosques, and the other half remained in use by the Christians. The church canons remained in force in all matters concerning the inner church administration, which was in the hands of the patriarch and bishops. The sacred patriarchal synod continued to exist, and the patriarch along with the synod carried on the matters of church administration. All religious services could be freely celebrated; in all cities and villages, for instance, Easter might be solemnly celebrated. This religious toleration in the Turkish Empire has been preserved to the present day, although in the course of time, cases of Turkish violation of the religious rights of the Christians became more frequent, and the position of the Christian population was from time to time very difficult.
The first patriarch of Constantinople under the new rule was elected by the clergy soon after the capture of the city by the Turks, and he was recognized by the sultan. The choice fell on Gennadius (George) Scholarius. He had accompanied John VIII to the Council of Ferrara and Florence and had been then a partisan of union, but later he changed his mind and became a zealous defender of Orthodoxy. With his accession, the Greco-Roman union entirely ceased to exist
For the "religious toleration" of the Turks, see George Horton's, The Blight of Asia: An Account of the Systematic Extermination of Christian Populations by Turks; cf. more web-sites on Turkey
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Reference address : https://www.ellopos.net/elpenor/vasilief/council-st-sophia.asp