The federal government recognized the loyalist legislature at the Wheeling Convention as the legitimate government of Virginia; when the loyalist government voted to permit West Virginia to secede, Congress considered that to satisfy the requirement of Art. IV §3.
I know you're only laying out the history, but just because the federal government "recognizes" something does not make it correct. The proper government of Virginia was the one elected under the auspices of the state constitution. The Wheeling Convention doesn't fit the bill.