John Milliton managed to clear his name and in 1548 he became High Sheriff of Cornwall. At the time of the Reformation, after the execution of Sir Humphrey Arundel for his part in the rebellion of 1549, Milliton became the Captain of St. Michael's Mount.
The alliance between the Millitons and the Godolphins was cemented by the marriage of William's daughter, Honor, to John's son and heir. Much refurbishment of Pengersick appears to have taken place in celebration of the event. It is said that the two loathed each other.
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