My understanding was that owen switched to Congregationalist to accommodate Cromwell.
Sadly it was during that time when he wrote on church polity.
Later he was persuaded back to presbyterian gvt being consistent with scriptures like Acts 15 etc.
I guess I'd like to know your sources. Owen was ordained in the Anglican Church during his time at Oxford, but later he refused to go along with William Laud's high church discipline. He left Oxford in 1637, spent a stint as a as a private chaplain for six years, became a Presbyterian and went to Fordham, Essex in 1643. He was called to a Presbyterian congregation as its pastor, and very soon thereafter introduced and advocated independent church government. He preached before the Long Parliament around 1646 clearing proclaiming his independent and Parliamentarian views. In fact he preached there in 1649 the very day following the execution of Charles I. In 1658 he took an active role in the Savoy Assembly from which came an Independent Church Confession. He became a leader of the Independents, became a pastor in 1673 of a large Independent congregation at Leadenhall Street Chapel and remained there until his death in 1683.
In 1680, toward the end of his life when he wrote his work, Union Among Protestants, he stated at one point therein: “Those who are for the Presbyterian form of an authoritative national church-state do, indeed, cut off and cast away most of those things which are the matter of contest between the present dissenting parties, and so make a nearer approach towards a firm union among all Protestants than the other do; yet such an authoritative church-state, in that form, is neither proper nor possible unto this nation, nor consistent with that pre-eminence of the crown, that liberty of the subjects, and freedom of the consciences of Christians, which are their due.”
Now, to be sure, I'm most willing to have any ignorance of mine concerning him corrected, but if he was ever persuaded back to Presbyterian polity, I know nothing of it.
DTK