Did s 48A operate even after Tribunal’s decision was substituted under s 417(1)?

The High Court of Australia (HCA) summarised the facts and arguments as follows:

1. 1. The appellant was refused a protection visa pursuant to s 65 of the Migration Act 1958 (Cth) ("the Act") by a delegate of the respondent, the Minister for Immigration and Multicultural Affairs ("the Delegate's Decision"). The Delegate's Decision was subsequently affirmed by the Administrative Appeals Tribunal ("the Tribunal") pursuant to s 415(2)(a) of the Act. The Assistant Minister for Immigration and Border Protection then decided to "substitute" the decision of the Tribunal with a more favourable decision made under s 417(1) of the Act – namely, to grant the appellant a Visitor (Subclass 600) visa for three months with a no further stay condition. Subsequently, the appellant made a further application for a protection visa, which was held to be invalid by a delegate of the Minister on the grounds that it was barred by s 48A of the Act.

1. 12. On appeal to this Court, the appellant pursued a single ground of appeal; namely, that the Full Federal Court erred in finding that the appellant's second application for a protection visa was invalid as it was barred by s 48A of the Act ...

Some of the questions to the HCA were as follows:

Question 1: Is the reference to the act of refusal in s 48A "simply to an historical fact, that has not been set aside in fact, regardless of its legal effect"?

Question 2: Does s 417 on its face confer a power of substitution only, instead of a power to set aside a decision of the Tribunal?

Question 3: Did the Assistant Minister's act of substitution in s 417(1) have the effect of setting aside the delegate's refusal decision?

The HCA answered those questions as follows: