I don't think the Virginia legislature approved the secession of West Virginia. I believe the reasoning was Virginia was not part of the US and therefore WV could be admitted. At least for this act, the independent sovereignty of the Confederacy was recognized.
Actually, Lincoln never recognized the sovereignty of the Confederacy, or that the Southern states had even seceded. Lincoln simply did whatever he wanted, and made up arguments to support whatever actions he took, regardless what the Constitution said.
-He suspended habeus corpus, without Congressional vote (clearly listed in the Constitution as Congressional, NOT presidential, authority). When the Chief Justice of the Supreme Court, named Tanney, came down with a ruling that Lincoln's actions were unconstitutional, Lincoln ordered the Chief Justice arrested. (When in the Course of Human Events, Charles Adams).
-Lincoln ended freedom of the press by presidential fiat. First, he sent Union troops to burn down the newspaper offices. When that proved unpopular, he sent federal troops to arrest the newpaper editors. His final tactic was to order the US Mail not to delivery papers for those newspapers that printed nasty things about him. During the war, about 300 northern newspapers were shut down.
The tyrrany of Lincoln goes on, and on, and on.....