In late 1641 when rebellion broke out in Ireland, the sisters evacuated their convent. It was raided and burned in 1642, with the sisters sheltering with their relatives and friends. The community had over 30 sisters at this time, with some moving to County Galway, and four moving to Wexford. Dillon remained in Athlone until 1653, being re-elected abbess at least five times. When Oliver Cromwell declared that all nuns were "to marry or leave the country" in 1653, Dillon led a group of nuns to Spain where they believed they would be welcomed into religious houses there. However, when they arrived at Galicia, their ship was quarantined and they were not allowed to land. While on board the ship, Dillon became sick and died, and is buried in Spain.