The second half of the 19th century witnessed the invasion of Protestant missionaries into the Malankara Syrian Orthodox Church. They had the support of the British. The Kottayam Cheriyapally was in the custody of the Protestants following a Court order.

Patriarch Moran Peter IV returned to Jerusalem in 1877 after conducting the Mulanthuruthy Synod (in 1876). In 1880, Mor Dionysius Joseph Pulikkottil (who was ordained by Patriarch Moran Yacoub II in 1865) and Mor Gregorios Geevarghese Chathuruthil (who was ordained by Patriarch Moran Peter IV in 1876) wrote a letter to the Patriarch Moran Peter IV describing the difficulties in the Malankara Church due to the Protestant schisms. Understanding the situation, Moran Peter IV ordained Ramban Shemvun by name ATHANASIUS and sent him to Malankara along with Deacon Sleeba (later the delegate Mor Osthatheos Sleeba). Ramban Shemvun had visited India in 1849 along with Mor Athanasius Sthepanose of Turab'din. They reached Kochi on January 1, 1881.

In 1879, Mor Dionysius Joseph filed a petition against Thomas Athanasius, the successor of Palakkunnath Mathews Athanasius for the recovery of properties in their custody. The Royal Court Judgement was in favour of Mor Dionysius Joseph in 1889. During this period (1881-1889) Mor Athanasius Shemvun was residing and conducting services at the Barsawmo’s Church (Puthenpally), Kottayam. The Kottayam Valiyapally was also then  under the custody of the Protestants except the vestry to the South of the church (Philip, 1993; Stephen, 2006).

Subsequent to the Royal Court Judgment, Mor Dionysius Joseph regained the Old Seminary and Mor Athanasius Shemvun shifted his residence to the Old Seminary, Kottayam. Mor Athanasius Shemvun departed for the heavenly abode on 11 June 1889 at the Old Seminary. The mortal remains were intered at the Northern side of the altar of Mor Barsawmo’s church (Puthenpally) Kottayam. The Foundation stone for Puthenpally was laid as per the direction of Mor Coorilos Yuyakim, the delegate of the Holy See of Antioch, on 15 February 1868 . The anniversary of Mor Athanasius Shemvun is celebrated on June 11.