After the death of El-Hakim in 1021, emperor Romanus III Argyrus and Ali az-Zahir, the son of El-Hakim, made peace in 1030. In the meantime, Patr. Nicephorus continued rebuilding the Church of the [[Church of the Holy Sepulchre (Jerusalem)|Holy Sepulchre]] that was being re-built after its destruction in 1009. In the re-building effort, Patr. Nicephorus was helped by Joannicus who would succeed him. However in 1034, Jerusalem was hit by an earthquake that substantially damaged the city and the Church of the Holy Sepulchre. Re-construction was going slowly.
in 1042, upon ascending to the throne of Constantinople, emperor Constantine IX Monomachos finally funded the reconstruction of the Church, as well as other Christian establishments in the Holy Land, under the treaty concluded earlier by Ali az-Zahir and emperor Romanus III. <ref>Ousterhout, Robert (1989). "Rebuilding the Temple: Constantine Monomachus and the Holy Sepulchre". Journal of the Society of Architectural Historians 48 (1): 66–78.
Patr. Nicephorus reposed in 1048.