That really doesn't seem legal. Wouldn't any government voted for by the constituents of only one small section of a state be, by definition, invalid, thus rendering any motions passed by that government invalid? And obviously a plebiscite in that region would be even more illegal.
Not really "small section". The voters of the western Virginia counties, at the time, comprised about a third of the total Virginia electorate. (Had slaves been counted, of course, the proportion would've shrunk rather dramatically. But they weren't.)
But I don't see how it could have been not legal. Insurgents, terrorists, and traitors prevented the due election of American state government officials in most of the Commonwealth of Virginia; the United States Army ensured that it was possible to elect them in the rest of it. That does not make those elections that
did successfully take place any less valid or legal. Had the inhabitants of the traitor counties of Virginia been even remotely interested in influencing the question of West Virginia's statehood or lack thereof, their inhabitants could've, I dunno, not tried to secede, and actually participated in state government.
Finally, after a late-1860s dispute over the status of two of West Virginia's border counties, the Supreme Court reaffirmed that those two counties
were, by rights, West Virginia's, and in the process confirmed the legality of West Virginia's creation in the first place. So there's that, too.
I suppose the issue is whether or not the people in the rest of the state had the opportunity to vote.
They were denied that opportunity by the Confederacy.
