Maybe you should have read that case? Because Clinton followed the law. The specific law that gave the Presidency line item veto power. The law suit wasn't really about him cancelling the debt New York City owed the federal government. It was about the line item veto power.
If it were about the money, him cancelling the debt would not have saved the government money. It cost the government money because they paid out and New York didn't pay it back.
So...he was following the law, using a power expressly given to the President, and that power was tested over that case. That power was found to be unconstitutional and was removed.
Which, for the record, I agree with. Presidents (nor governors) should have line item veto power.