On 7 July 1567 a decree of the senate was issued referring the matter to a committee, Hughes to be bound by its decision without appeal.
At the earl's suggestion the matter was left to him, Sir William Cecil, then chancellor of the university, and Archbishop Matthew Parker.
Parker advised that he should be restrained from preaching; but the concrete result was an order of the chancellor against questioning the article.
[2] Hughes gave assistance to William Morgan in his translation of the Bible into Welsh; and made an issue of having Welsh-speaking priests.
The report dated 24 February 1587, described the bishop as holding in commendam, with the archdeaconry and the rectory of Llysvaen, which he held by virtue of a faculty obtained in 1573, 15 livings.
[2] In October 1600 Hughes died, and was buried in the choir of St Asaph Cathedral.
By his wife Lucia, daughter of Robert Knowesley of Denbighshire, he left a son, William, and a daughter, Anne, who married Thomas, youngest son of Sir Thomas Mostyn.