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When the church or chapel that was built when St. Nicholaos died was destroyed in the earthquake of 529, a larger, perhaps basilica-type church was built. Peschlow estimates that the large part of the north side of today's building belongs to this first building, with two small spaces with equal apsis on the south side of the large apse.
This church was destroyed in the 8th century by Zelzah or Arabian invasions, and then renewed again. It was destroyed by the influx of the Arab Navy from the sea in 1034. The church which remained in ruins for 10 years, the Byzantine Emperor IX in 1042. It is understood from the inscription that it was repaired by Constantine Monomakhos and his wife Zoe. In the 12th century some additions to the building were made, and the church was repaired.