However, two months after the assumption of his duties as Dean, he was faced with unforeseen developments in terms of the function and the future of the School, due to unfavourable conditions that developed in the life of the Ecumenical Patriarchate and the Greek faithful of Constantinople which naturally affected the smooth function of the School, which is its eminent institution. These developments ensued after the unprecedented and awful events of September 6-7, 1955, which were perpetrated against sacred churches, institutions, educational or not, and the property of the Ecumenical Patriarchate and its flock, and derived from the Cyprus issue. Therefore, and in light of the anticipated negative consequences and ramifications on the function of the School, the concern and attention of the new Dean, Archimandrite Maximos were directed to the handling, and primarily to the strict adherence and undeviating implementation of the Regulation that was ratified by the Turkish government, so that there would be no cause raised for the suspension of the School, and the new functioning academic system – an accomplishment of his predecessor Metropolitan Iakovos – would have to be completed at any sacrifice.
The stance taken by Archbishop Makarios on the Cyprus issue, resulted in the continuation of the hard circumstances affecting the life and being of the Ecumenical Patriarchate and its flock, and the completely unfavourable dispositions and manifestations of the Turkish state against them both, and mostly against the clergymen and the School that educated them. Under the new Dean’s Archimandrite Maximos Repanellis’ tireless management and fighting vigour, the School carried on its regular function during this most difficult four-year period (1955-1959) despite the continuously intensifying inspections on the part of the Ministry of Education, in seeking and possibly discovering any omissions in the implementation of the functioning Regulation of the School. The function of the School became more challenging because of the imposed bans on various events and practices, inside and outside it, that were essential for the education of student, as future clergymen, until the restoration of the friendly relations between Turkey and Greece, after the signing of the treaties of Zurich and London in February 1959, on the settlement of the Cyprus issue.
The restoration of these relations had a direct impact on the stance and disposition of the Turkish state toward the School, thereby lifting many restraining measures from its function. Unfortunately, the ensued events, within a short period of time, namely the overthrow of the Turkish Government by the militia and the governing of the Country by them, in May 1960, and the reoccurrence of conflicts and disputes in the newly-established Republic of Cyprus, beginning in December 1963, led anew to the worsening of the relations between the two countries and, consequently, to the announcement and imposition of new restrictive measures against the School’s function.
The toughest measure of all was the ban imposed by the Ministry of Education, starting with the academic year 1964 – 1965, on the recruitment and enrolment to the School of students from abroad, from where the largest number of students originated at approximately eighty-five per cent. This ban was a big and strong blow against the School’s function, as a pan-Orthodox theological school, and seemed like a prelude to the beginning of the end for it.