Yes he did. As president he had authority over all the United States. Even those engaged in rebellion.
“Yes he did.”
If he had authority over the Confederacy then his Emancipation Proclamation would have freed the slaves. It freed no one, and you know it. You can cover your ears and chant “lalalalalalalalalala” all you want, but the fact remains the Confederate States of America was a separate and sovereign nation for the four years it existed. The only influence Lincoln had over it was at the point of a gun.