> As in the government’s position was yes he is in prison for something that isn’t illegal, but he had already used up his appeals.

This is the position of the Eighth Circuit and seems to be the likely eventual position of the conservative Supreme Court justices, but the government's position is actually a bit more nuanced: yes his existing conviction would no longer be upheld under more recent statutory interpretation, and he should be granted an extra appeal if he could actually demonstrate his innocence under the new interpretation, but what he did would probably still be considered illegal when all available facts on the record are considered and so he wouldn't satisfy what the government considers a reasonable threshold for an extra special appeal.