That's an exactly wrong read on what this case does.
There are two separable issues in this case. One is incorporation, the other is whether nunchaka count as "arms".
Per Eugene Volokh and the legal minds at Volokh Conspiracy it is likely the Supremes would affirm incorporation but remand on whether nunchaku are "arms" under Heller.
It didn't "lose incorporation", the 2nd Circuit merely ruled that Presser still stood. This sets up exactly the inter-circuit controversy we need to have the USSC rule.
Right now we have the 9th saying Incorporated and that Presser was wrong, and their (convoluted but clever) reasoning hands the Supremes a way to set aside Presser and avoid stare decisis. Given the depth of their Heller ruling that's a hole the Supremes will walk right on through. Also remember the panel that wrote Nordyke was headed by a Clinton appointee, it wasn't a "right-wing" decision.
Regardless of how well or sincerely this guy's counsel does in presentation, the Supremes can pull any ruling they can justify out of the argument. His attorney can simply say "2nd is Incorporated", which is the guy's argument, and rest his case. It doesn't matter what the State of NY says at that point. If the Supremes want Incorp (which I think they do) they can then say, "Yep, via x, y and z, Plaintiff is correct, 2nd is incorporated, remand for determination of whether nunchaku are "arms" under the 2nd".
Also remember that prior to this case hitting the USSC there is one in the 7th awaiting a decision that could also support Incorporation. That would create a "majority" of post-Heller decisions on the topic that the Supremes could cite to simply ratify nationwide.
