The substance of the revision was to reformulate the Westminster Divines' teaching on the civil magistrate. The Westminster Assembly had been called by Parliament, and its affirmations about the role and function of the government, especially in ecclesiastical matters, reflected a situation in which the state exerted control over the church as part of the price of religious establishment. The American revision of 1787-1789 took into account the new situation in the United States, where the state had no authority over the church.
The most notable revisions were made in the chapters on the civil magistrate and synods and councils in the Confession of Faith. In the original version of chapter 23, the Divines declared that "for the better effecting whereof, [the civil magistrate] has the power to call synods, to be present at them, and to provide that whatsoever is transacted in them be according to the mind of God" (23.3). Reverence for George Washington aside, the prospect of giving him the power to call an assembly or synod did not make much sense by 1789. So the American revision changed that section to assert that civil magistrates, as "nursing fathers," had the duty "to protect the church of our common Lord, without giving the preference to any denomination of Christians above the rest, in such a manner that all ecclesiastical persons whatever shall enjoy the full, free, and unquestioned liberty of discharging every part of their sacred functions, without violence or danger" (23.3). Gone was the power of the state to convene an assembly and the duty to insure that such church bodies conducted their business "according to the mind of God."
Furthermore, the American revision went on to affirm the principle of religious freedom and asserted that the civil magistrate had a duty to protect that liberty, even including the freedom of infidels: "It is the duty of civil magistrates to protect the person and good name of all their people, in such an effectual manner as that no person be suffered, either upon pretense of religion or of infidelity, to offer any indignity, violence, abuse, or injury."
American Presbyterians undertook a similar revision in chapter 31 on synods and councils. Here they deleted entirely section 2 from the original version, which gave further direction to civil magistrates about their participation in ecclesiastical assemblies. The civil magistrate was mentioned in the revised chapter only in paragraph 4 (old number 5), which now stated that the church is not to "handle or conclude" any matter of civil polity, except for "cases extraordinary," to satisfy the conscience of the church, or to comply with a request from the civil magistrate.