Just as Article IV, Section III prohibits forming a new state from being created from a portion of another state nor from two or more states without the consent of all the state legislatures involved, plus that of Congress.
Since the West Virginia counties chose to secede from the Confederacy and throw in their lot with the Union, it would have been unconstitutional and illegal for their new state to have been so created- unless, in accordance with the Constitution, the Virginia legislature was no longer a part of the government of the United States, but was by then a creature of the Confederacy.
U.S. Constitution, Article IV, Section 3. New states may be admitted by the Congress into this union; but no new states shall be formed or erected within the jurisdiction of any other state; nor any state be formed by the junction of two or more states, or parts of states, without the consent of the legislatures of the states concerned as well as of the Congress.
West Virginia was organized by the legitimate legislature of the state of Virginia, and thus its existence was approved by the legislature of VA and of WV and was approved by Congress.