DiogenesLamp: "Well if that is true, how did Lincoln revoke Article IV, section 2?
If they were always part of the Union, the constitution required him to return their slaves, and it doesn't mention any exceptions to this rule."
Regions in rebellion were covered by the 1807 Insurrection Act:
Lincoln certainly did not "revoke" Article IV, section 2 for states & regions which remained loyal.
But regions in rebellion were subject to the words, "as he considers necessary", including, for examples, blockade and contraband.
DiogenesLamp: "The only argument on behalf of the legitimacy of his act is that they were no longer under the law of the US constitution."
The Constitution recognizes that rebellion is a different status, for example, in Article 1, section 9:
DiogenesLamp: "So which is it?
Either US Constitutional law didn't apply to them, or Lincoln violated Constitutional law."
Rubbish, the Constitution does not require people in rebellion to be treated the same as normal citizens.
DiogenesLamp: "The puppet government's put in place by the military forces occupying those lands voted in the way the puppets were told to vote.
This does not represent an actual consent, it was deliberate coercion that people pretended was a legitimate expression of the will of the people of those states."
"Puppet government" is incorrect.
Those state governments were elected by voters in good standing at the time, meaning rebels were not allowed to vote.
So there was no coercion regarding the 13th Amendment, since the authorized voters were more than eager to see it ratified.
But the key point regarding ratification of the 13th, 14th and 15th amendments is that, in the end, every state which could did ratify them and no state ever revoked its previous ratifications on grounds they were "coerced" or in any other way illegitimate.
So the amendments stand as ratified, according to the original intents of their authors, though not necessarily some later fanciful judicial reinterpretations.
Acts of congress do not overturn Natural Law rights which were the entire foundation of the USA's existence.
Look up "Declaration of Independence" for a refresher course on what "Natural rights" mean.
And it wasn't a "rebellion" it was a divorce, but some people refused to stay on their side of the border.