The difference in legal tactics of current times and civil war
*Then : an entire judicial system was set up and United States legal system was ignored. It was replaced with laws reflecting the confederate beliefs Now : The opposition has installed Judges within the system who legislate from the bench.
This is a change reflected after the lessons learned post war.
The Union took extra care as to never acknowledge the existence of a Confederate Judiciary and treated the Confederate States as a Military arm only so as not to give legitimacy to the Government. Lincoln ignored orders coming from Judges seen to sympathize with the Confederates.
*Then : All decisions that arose from the Confederate Courts were repudiated by 1868 and all Judges who did not swear allegiance to the United States Constitution were worked off the bench. Now : TBD but we can expect a similar outcome. Lincoln gave blanket pardons to sympathizers provided they swore and Oath to the U S so I can only presume the Judges that were allowed to continue were given the same. There are very few legal documents available regarding the Confederate Judiciary as they were mostly destroyed during the war.
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Then : The Supreme Court ruled post war that all States were part of the Union and the secession was never legal, therefore, no laws created were binding and everything reverted back to pre war law.