Yet New York’s ratification was accepted despite it making an express reservation at the time of ratification stating that it retained its ultimate sovereignty and could resume the powers it delegated to the new federal government. If states could not do so, if they were agreeing to bind themselves forever, why did nobody say the ratifications of New York and Virginia and Rhode Island were defective and could not be accepted?
You have that backwards. Nobody "accepted" New York's ratification or any other state's ratification. On they contrary, they were the ones doing the accepting. By ratifying the Constitution they were accepting its supremacy and agreeing to abide by it's constraints.