Which doesn't cancel the Constitution, but instead calls for corrective action by a later Congress, which should deprive West Virginia of its seat in the Union and reunite it with the Richmond government.
Break out those old 49-star flags, and put away the 50-star flags until Puerto Rico changes its mind.
The Supreme Court recognized the constitutionality of the existence of West Virginia when it agreed to hear the case of Virginia v West Virginia in 1871.
It's possible that a later Virginia legislature officially endorsed the separation of West Virginia (as if they had any choice by then). Lincoln may have treated the rump VA legislature as legally entitled to act for the state, but I don't think Congress treated it as a valid state government in other respects. Economically, Virginia is probably better off without its lost counties.