Church split into two factions one supporting naveekaranam (reformation) and the others who was against it, following a court order. As a result, reformist faction established them self as separate church known as Malankara Marthoma Syrian Church . The Kochupalli in Kozhencherry was among the few churches allotted to the Marthoma church. Afterwards, the Marthomites and the Orthodox believers conducted their worship in the Kochupalli taking turns. In 1069 M.E. (1893) the church was renovated. On the northern side of the compound wall, where the old church had existed, a piece of land was set apart for use as a cemetery. The expenses were met by the Marthomites. On finishing the work, the Orthodox were asked to meet a share of the expenses which was not obliged to by them. A court case was filed and the judgement asked the Orthodox to remit a share of the expenses if they were to conduct worship once in five times. But the orthodox were not prepared to comply with it. They secured a place of their own and established a parish church, which they could use with full freedom. This left the Kochupalli exclusively to the Marthomites. As the large majority of Christian families of this area continued to support Naveekaranam, the number of parishioners increased and the Kozhencherry Church grew stronger day by day. St. Thomas Marthoma Valia Pally, Kozhencherry In order to accommodate the increasing number of parishioners, it became inevitable to enlarge the Kochupalli. But there was strong opposition from the parishioners about demolishing the Kochupalli. Many of them wanted the Kochupalli to be kept intact as it was one of the very few buildings representing the antiquity and the treasured traditions of the Mar Thoma church. However, Edavaka sangham, the Parish General Body was aware of the inadequacy of the available plot and it was decided to secure a new plot and construct a new bigger church. Some were of the opinion that if a plot adjoining the church ground on the western side was purchased there would be enough space to construct a new church. But there was a pathway in between the two plots. The intervention of the influential Rev. C. P. Philipose was instrumental in arranging a new pathway in place of the old one. After this, the Mannurethu plot on the western side of the church was bought and under the inspiring leadership of