Lincoln, and the Federal Government, always saw the Southern States as part of the United States. They never recognised them as a separate country. Some part of America was under rebellion.

Legally, what Lincoln did with the Emancipation Proclamation, he could have done earlier in the war. However, he was focused on building and maintaining an extremely fragile alliance with some border states where slavery was still legal. Plus the Democrats in the North whom he needed their support in Congress.

Lincoln was elected on the platform that he would leave slavery alone where it already was. His platform was only to stop its expansion into further territories. He knew the South might start a war but didn’t think it overly likely. He did not come into the office with some scheme to immediately abolish slavery in the South. He spent the first year and a half of the war trying to get the South to stop fighting with the plan that they could keep their slaves. The Emancipation Proclamation was a great act. But it committed Lincoln to a fight to the very end. There could no longer be a truce and go back to how things were.