The church at Ballyduff was lost so completely that when the antiquarian John O'Donovan visited in August of that year he could find no trace of any standing structure. What he and earlier observers had not realised was that the building had not so much disappeared as been redistributed, its dressed red sandstone blocks quietly absorbed into the fabric of the surrounding burials.

By 1615 the parsonage here, described as Sir Richard Boyle's gift, was recorded during a Royal Visitation as "waste and worth nothing." Boyle, later the first Earl of Cork, had accumulated enormous landholdings across Munster following the Elizabethan plantations, and the fate of small rural parishes in his gift was often determined more by economics than pastoral care. The church itself still appeared in a diocesan list in 1622, and when Samuel Lewis wrote his topographical account of Ireland in 1837, he noted ruins in the ancient burial ground, with tithes of £55 payable to the Earl of Cork as impropriator, meaning the rectorial income had been diverted to a lay owner rather than a resident clergyman. Within four years, O'Donovan found nothing at all. A survey carried out by Laurence Dunne in 2010 recovered, for the first time, the basal courses of the south and east walls, the south wall running some eleven metres from the south-east corner and measuring just over a metre thick. Forty-three architectural fragments were recorded across the graveyard, most of them reused in tomb construction. Among the most significant is the head of a finely carved ogee window, a type characterised by its double-curved arch, which dates to the fifteenth century and now serves as a grave marker near the east side of the burial ground. A complete holy water stoup, of the projecting basin type rather than one set into a wall, was also found repurposed as a burial marker nearby, all of it cut from the same local red sandstone as the rest of the church.