What was Lincoln's reason for emancipating slaves in the Confederacy?
To turn the war into an official crusade against slavery, so that Britain and France could not aid the South without looking pro-slavery themselves.
Because he had to be diplomatic towards influential slave-owners in the four buffer-states, in case they turned against him and joined the Confederacy. Note that the Proclamation did not strictly free the Southern slaves. It just gave his troops the wartime power to pillage the farms and free the slaves, on the grounds that slaves were enemy property.