I believe the Constitution is still in force.
For the rest of us, current law is 28 USC 1251.
For some of us the Constitution is still the current law.
If 28 USC 1251 purports to give Susan Bolton jurisdiction to determine a lawsuit by the United States Government against the State of Arizona, then 28 USC 1251 is unconstitutional and any ruling she made on the case is void.
You are correct that the Constitution was not properly amended to permit other than Scotus to hear a case between the US and a state.
There is no such amendment.