[1] In 1648, when the Parliamentary visitors came to the college, and Ellis was asked whether he meant to submit to the authority of Parliament, he replied that he could not "without the hazard of shipwrackinge of my soule".
He hoped to be appointed to succeed Mansell in 1661, but the position went to Leoline Jenkins and Ellis then gave up his teaching duties (although he retained his fellowship until 1667).
However, in 1663, after 128 sheets of the book had been printed, Ellis complained that all of Vaughan's material had been published in 1661 by Percie Enderbie and refused to continue.
[1] In 1665, King Charles II, his court and Parliament moved to Oxford to escape the plague, and Ellis's fortunes improved.
He succeeded his kinsman John Ellis as rector of St Mary's, Dolgellau, Merionethshire.