There are a couple of technical issues in the question, one relates to "secession" and the state of America at the time of formation of West Virginia. The other revolves around the post-war view of the seceding states during the war.

Before West Virginia left the state of Virginia, the state of Virginia intended to leave the United States of America. This presented those in West Virginia with few options. One would be a ethically defined revolution against the United States in unilateral secession (even if they intend to reunite), the Confederate States due to impending secession, as well as their fellow Virginians (as in they don't entrust their right to vote). The second would simply be wait for Virginian independence (should it even happen after a state referendum) before seceding.

However, any other solution was taking far too long, so they decided to "wait and see", and Virginia "legally" seceded from the Union without a vote. This basically remained unrecognised in the west though.

Then a weird situation ended up where Virginia was being governed by the Union and Confederacy, because secession from the Union was not approved by popular vote.

Now the Union ran into the problem of the Confederacy. If West Virginia was seen as seceding from Virginia it would legitimise the Confederacy as a sovereign nation. Civil war, would just become war.

So this helped develop the view that the secession never happened. To this end, the pro-Union legislature (which was empty of Confederates who did not recognise it) approved a vote to create a new state, the Union flooded the state with soldiers to vote in the creation of a new state, which was quickly admitted to the Union.

TL;DR When the war developed secession became acknowledged as unconstitutional. Therefore West Virginia did not secede, rather was created by the creation of a new state, as guaranteed in the constitution.