The state of Virginia was in no position to dictate terms. They accepted the Constitution as ratified and that document has no provisions for states to resume powers granted to the federal government, regardless of their ratification document.
When two parties agree on something and exchange correspondence in relation to a contract, one party or both will state in writing what they agree to. Virginia did that. Since the Feds didn't object, silence is construed as acceptance under the law.
You can slice it anyway you want, but it you can't disprove it.