The Amendment Disappears
In 1829, the following note appears on p. 23, Vol. 1 of the New York Revised Statutes: "In the edition of the Laws of the U.S. before referred to, there is an amendment printed as article 13, prohibiting citizens from accepting titles of nobility or honor, or presents, offices, &c. from foreign nations. But, by a message of the president of the United States of the 4th of February, 1818, in answer to a resolution of the house of representatives, it appears that this amendment had been ratified only by 12 states, and therefore had not been adopted. See Vol. IV of the printed papers of the 1st session of the 15th congress, No. 76." In 1854, a similar note appeared in the Oregon Statutes. Both notes refer to the Laws of the United States, 1st vol. p. 73(or 74).
It's not yet clear whether the 13th Amendment was published in Laws of the United States, 1st Vol., prematurely, by accident, in anticipation of Virginia's ratification, or as part of a plot to discredit the Amendment by making is appear that only twelve States had ratified. Whether the Laws of the United States Vol. 1 (carrying the 13th Amendment) was re-called or made-up is unknown. In fact, it's not even clear that the specified volume was actually printed -- the Law Library of the Library of Congress has no record of its existence.
However, because the noted authors reported no further references to the 13th Amendment after the Presidential letter of February, 1818, they apparently assumed the ratification process had ended in failure at that time. If so, they neglected to seek information on the Amendment after 1818, or at the state level, and therefore missed the evidence of Virginia's ratification. This opinion -- assuming that the Presidential letter of February, 1818, was the last word on the Amendment -- has persisted to this day. In 1849, Virginia decided to revise the 1819 Civil Code of Virginia (which had contained the 13th Amendment for 30 years). It was at that time that one of the code's revisers (a lawyer named Patton) wrote to the Secretary of the Navy, William B. Preston, asking if this Amendment had been ratified or appeared by mistake. Preston wrote to J. M. Clayton, the Secretary of State, who replied that this Amendment was not ratified by a sufficient number of States. This conclusion was based upon the information that Secretary of State John Quincy Adams had provided the House of Representatives in 1818, before Virginia's ratification in 1819. (Even today, the Congressional Research Service tells anyone asking about this 13th Amendment this same story: that only twelve states, not the requisite thirteen, had ratified.)
However, despite Clayton's opinion, the Amendment continued to be published in various states and territories for at least another eleven years (the last known publication was in the Nebraska territory in 1860)
Once again the 13th Amendment was caught in the riptides of American politics. South Carolina seceded from the Union in December of 1860, signaling the onset of the Civil War. In March, 1861, President Abraham Lincoln was inaugurated.
Later in 1861, another proposed amendment, also numbered thirteen,
was signed by President Lincoln. This was the only proposed amendment that
was ever signed by a president. That resolve to amend read:
"ARTICLE THIRTEEN, No amendment shall be made to the Constitution which will authorize or give to Congress the power to abolish or interfere, within any State, with the domestic institutions thereof, including that of persons held to labor or service by the laws of said State." (In other words, President Lincoln had signed a resolve that would have permitted slavery, and upheld states' rights.) Only one State, Illinois, ratified this proposed amendment before the Civil War broke out in 1861.
In the tumult of 1865, the original 13th Amendment was finally removed from the US Constitution. On January 31, another 13th Amendment (which prohibited slavery in Sect. 1, and ended states' rights in Sect. 2) was proposed. On April 9, the Civil War ended with General Lee's surrender. On April 14, President Lincoln (who, in 1861, had signed the proposed Amendment that would have allowed slavery and states rights) was assassinated. On December 6, the "new" 13th Amendment loudly prohibiting slavery (and quietly surrendering states rights to the federal government) was ratified, replacing and effectively erasing the original 13th Amendment that had prohibited "titles of nobility" and "honors".