A Court cannot reach an act of Congress unless it is unconstitutional. Removing the penalty was not an unconstitutional act, though it had the (alleged) effect of making the ACA unconstitutional. It's kinda weird to wrap your head around, but I guess you could say that Congress acted with the intent that the ACA be unconstitutional? Kind of a procedural end-run around actually, fully repealing it in Congress. Impressive feat, if true. Courts generally defer to the most recent actions from the Legislative Branch when construing legislative intent. So, if a later amendment contradicts the intent of the Congress that passed the underlying act, courts assume that the later Congress did so intentionally and will not disturb the later act unless it be unconstitutional. It's a separation of powers thing.
That said, I don't think the result reached in this case is necessarily compelled, and a Judge in a different part of the country may well have reached a different conclusion.
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