The organization of the eparchy was extraordinarily handicapped by the outbreak of World War I, its protraction, and the increasingly severity of the economic situation. Due to the wartime conditions the government was not able to meet its obligations. The delay in the construction of the seminary and the bishop’s residence especially caused significant difficulties. The eparchy was not provided with sufficient income. This was somewhat alleviated by the bequest of Arkád Pásztory, a basilian monk, who had not joined a monastery, and who in 1915 donated 2,000 “hold” [one hold equals 0.57 hectares] of plow land, 300 “hold” of forest and vineyards, as well as farm buildings, to the Eparchy of Hajdúdorog. With the assistance of Antal Papp, Bishop of Munkács, the seminarists of the eparchy were educated in the seminary in Ungvár. In accordance with the request of Bishop Miklósy, the leadership placed particular emphasis on the appropriate learning of Ancient Greek by the priests of the Eparchy of Hajdúdorog, as the bull establishing the eparchy had directed. He also made certain that the Hajdúdorog clergy learn the hymns not in Old Church Slavonic, in the manner of the priests of Munkács and Eperjes,
because they would have no use for that, but in Hungarian, based on the Danilovics hymnal. The formation of clergy became ever more problematic because due to the war the school year became considerably shorter than usual.
The meetings held by the three prelates Antal Papp, István Miklósy and István Novák in Nyíregyháza in 1916 and 1918 expressed the close connection with the eparchies of Munkács and Eperjes. At the first meeting the bishops decided to implement the use of the Gregorian calendar, which was introduced on 24 June 1916. This occurred without any difficulties in the Eparchy of Hajdúdorog but in the Munkács and Eperjes eparchies serious resistance developed. Consequently in 1918, in Munkács they returned to the Julian calendar and in Eperjes they made the use of the Gregorian calendar optional. At the meeting in 1918, they consulted on the issues of the Hungarian speaking Greek Catholics, who had not been included in the Eparchy of Hajdúdorog, on the extension of the validity of the canon law codex of 1917, and on the questions relating to the retirement benefits of the priests and the widowed clergy. The promising cooperation of the three Greek Catholic Bishoprics was broken apart by the changes that accompanied the end of the World War.
The chaos that followed the military collapse in 1918 immediately made itself felt in the Eparchy of Hajdúdorog. Under the leadership of Romulus Marchiş, parish priest of Nagykároly and Archdean of Szatmár, a group of the parishes that had earlier belonged to the Eparchy of Nagyvárad declared unilaterally that they were no longer a part of the Eparchy of Hajdúdorog. Through the nuncio they asked the Holy See to create a vicariate for all of the parishes that had formerly belonged to the Bishopric of Nagyvárad. Bishop Radu formally distanced himself from this unilateral step, which was in serious conflict with canon law, but asked the Holy See to be made the legally constituted ordinary of these parishes. Bishop Miklósy asked for the strict punishment of the rebellious archdean. Encouraged by the successes of the Romanian offensive, which had started in the spring of 1919, bishop Radu repeatedly urged the Holy See to reply. The Romanian troops capturing Nyíregyháza took bishop Miklósy to Debrecen and tried to force him to voluntarily turn over the forty-four parishes. The nunciature was no longer able to keep in contact with bishop Miklósy, and the Hungarian government provided no replies to the requests of the Holy See. Since the territories of the parishes in question had in fact been placed under the supervision of the Romanian army, the Holy See ordered them under the jurisdiction of the Bishop of Nagyvárad on 10 May 1919. A few months later, Vasile Suciu, the Protosyncellus of the Metropolia of Fogaras-Gyulafehérvár, requested the return of the thirty-five parishes of the forane vicariate of the Székely region to the metropolia, and on 29 June the Holy See ordered it to be so.