You are getting the two generations of John Radcliffe (father and son) confused.
John Radcliffe d.1701, of Crot-y-Lough, and wife Margaret Cannell were the parents of:
1.Thomas Radcliffe - the eldest son - who was entered for Crot-y-Lough in 1705, and who on 6 May 1718 married his cousin Alice Radcliffe the second daughter of John Radcliffe of Belfast and his wife Jane Teare. It was this Thomas and his descendants who were known as y Vayr in the Andreas parish register. D.S. Dugdale wrote “On the 1727 Manorial Roll Crot-e-Lough was possessed by Thos Radcliffe. The home of the Ratcliff y Vairs was at Ballavarry gate, across the road from Belfast”.

It was John's father who left the croft to his wife while she lived and then to his eldest son John, "and in case his said son die before he come to lawful years, then his will was that it should [go to] his second son, & son from child to child". It wasn't left to a second son, because John the eldest survived to lawful years, but died in 1701 while his children were under age.

When John died in 1701 his two brothers Thomas and James were their supervisors as next of kin [James being the baby born after his father John's death]. Constance R. believed that this James was James of Bride d.1758, and that Thomas was the one in Lezayre, but we have found nothing to confirm this theory.

Sue