The President should inform the courts to enforce the Flores ruling by doing what he wants.
Some idiot federal judge can issue a piece of paper ordering the President not to do something, but if he disagrees, the court has no real power to bring an uncooperative executive branch to heel. The only available remedy is impeachment.
Good luck with it in the middle of a power struggle between two branches of government.
And its one the courts are likely to lose.