In other words, were the Confederate states officially no longer US states during the Civil War (as judged by the US government, then and now)?
In 1863, West Virginia joined the Union and remains a state to this day. However this is plainly unconstitutional (Article IV, section 3) unless we are to assume that Virginia was officially not a US state at the time.
Obviously, Virginia was de facto not a state, but it seems like the secession was not legally recognized at the time. If it were, it seems that might have all sorts of implications for laws enacted in those states before the Civil War and for the legality of secession.
I recently answered a similar question here about the constitutionality of West Virginia becoming a state.
Lincoln himself summarized the illegality of secession in his first inaugural address:
Again, if the United States be not a government proper, but an association of States in the nature of contract merely, can it, as a contract, be peaceably unmade, by less than all the parties who made it? One party to a contract may violate it---break it, so to speak; but does it not require all to rescind it?
Descending from these general principles, we find the proposition that, in legal contemplation, the Union is perpetual, confirmed by the history of the Union itself. The Union is much older than the Constitution. It was formed in fact, by the Articles of Association in 1774. It was matured and continued by the Declaration of Independence in 1776. It was further matured and expressly declared and pledged, to be perpetual, by the Articles of Confederation in 1778. And finally, in 1787, one of the declared objects for ordaining and establishing the Constitution, was ``to form a more perfect union.''
But if destruction of the Union, by one, or by a part only, of the States, be lawfully possible, the Union is less perfect than before, which contradicts the Constitution, and therefore is absurd.
It follows from these views that no State, upon its own mere motion, can lawfully get out of the Union,---that resolves and ordinances to that effect are legally nothing; and that acts of violence, within any State or States, are insurrectionary or treasonable, according to circumstances.
I therefore consider that the Union is unbroken; and, to the extent of my ability, I shall take care that the laws of the Union be faithfully executed in all the States. Doing this I deem to be only a simple duty on my part; and I shall perform it, unless my rightful masters, the American people, shall withhold the requisite means, or, in some tangible way, direct the contrary.
The creation of West Virginia was constitutional because , as the government in Richmond had no authority to leave the Union, the government in western Virginia that stated itself loyal was therefore the actual constitutional one. It was that elected government which began the process of creating a separate state, West Virginia.