The checks and balance are between the 3 branches of government. If congress wanted to stop the war, they could. If the supreme court wanted to hand the power to start wars back to congress they could.

Just because they don't, doesn't mean they aren't able. The real flat earth theory is thinking that unwritten rules and institutions were protected from a president that insists on pulling every lever of power at once, but that's separate from the checks and balances.