So the fact that Virginia added that disclaimer to her ratification document is meaningless if Virginia chose to resume those powers, i.e. secede, in a manner that was illegal under the Constitution she agreed to be bound by. As it happens, unilateral secession as practiced by the Confederate states was not legal. Madison said so long before the Southern rebellion. Chase said so in the Texas v. White decision after the rebellion was over.
The fact that a treaty or in this case was legally binding upon the citizens of the state in no way indicates that the state was agreeing to forever bind itself and surrender its sovereignty. Any law passed by the state government that does not conflict with the state constitution is binding upon the citizens.