What had declared the Southern states out of the Union? It wasn't the Reconstruction acts. I'm not aware of a single piece of legislation that ever referred to the Southern states as former states or territories.
And that, my friend, is at the heart of the argument that the 14th amendment was never legally ratified.
The state of New Jersey originally voted to ratify the 14th, but when its representatives observed the methods that its proponents were using to coerce the Southern states into ratification, NJ rescinded its ratification (to no avail). Herewith, NJ's reasons for its rescission:
"That it being necessary by the Constitution that every amendment to the same should be proposed by two thirds of both houses of Congress, the authors of said proposition, for the purpose of securing the assent of the requisite majority, determined to, and did, exclude from the said two houses eighty representatives from eleven states of the union, upon the pretense that there were no such states in the Union; but, finding that two thirds of the remainder of the said houses could not be brought to assent to the said proposition, they deliberately formed and carried out the design of mutilating the integrity of the United States Senate, and without any pretext or justification, other than the possession of the power, without the right, and in the palpable violation of the constitution, ejected a member of their own body, representing this state, and thus practically denied to New Jersey its equal suffrage in the senate, and thereby nominally secured the vote of two thirds of the said houses."
Hence, the U.S. Congress considered the southern states as having never left the Union only until such time as it became politically expedient to declare that that they had.