One, you are removing the context of the decision. US Airways was a defendant in that case and filed a Motion to Dismiss because it wasn't a party to the injunctive relief claims and had committed no torts against the Addington plaintiffs, so dismissal was proper because the court did lack subject matter jurisdiction over the company in those claims.
Two, as others have said, all the rulings made by Judge Wake in Addington v. USAPA are gone. Poof. Gone. This is a new case and the company is the plaintiff seeking declaratory relief.
An interesting point, however subject matter jurisdiction is not dependant on what type of hat the party wears; plaintiff or defendant. Subject Matter Jurisdiction pertains to whether or not the court has any authority to decide the dispute in question. Judge Wake has alreday dismissed on those grounds. While you are correct that the Addington litigation is no longer pending and therefore moot, subject matter jurisdiction was still found to be lacking and will likely be found again.
Consider; the company's complaint depends upon the findings of a jury trial that has been dismissed and the actions of the 9th did not clarify the merits of this case. Now there is no case and therefore there is no dispute over subject matter jurisdiction, there simply is no dispute to have a jurisdictional argument over.
The parties are free to bargain and are always subject to the duty of fair representation.
SUBJECT-MATTER JURISDICTION
http://topics.law.cornell.edu/wex/Jurisdiction
Subject matter is the cause, the object, the thing in dispute.
The authority of a court to decide a particular type of case is called subject- matter jurisdictionand is is set by the federal or state Constitution, or by state statutes.
It is a fatal objection to the jurisdiction of the court when it has not cognizance of the subject-matter of the action; as, if a cause exclusively of admiralty jurisdiction were brought in a court of common law, or a criminal proceeding in a court having jurisdiction of civil cases only. In such case, neither a plea to the jurisdiction, nor any other plea would be required to oust the court of jurisdiction. The cause might be dismissed upon motion, by the court, ex officio.
Subject matter jurisdiction is the court's authority to decide the issue in controversy such as a contracts issue, or a civil rights issue. State courts have general jurisdiction, meaning that they can hear any controversy except those prohibited by state law (some states, for example, deny subject matter jurisdiction for a case that does not involve state citizens and did not take place in the state) and those allocated to federal courts of exclusive jurisdiction such as bankruptcy issues (see 28 U.S.C. § 1334). Federal courts have limited jurisdiction in that they can only hear cases that fall both within the scope defined by the Constitution in Article III Section 2 and Congressional statutes (See 28 U.S.C. §1251, §1253, §1331, §1332).
Congressional Statutes, such as the Railway Labor Act prevent the courts from interfering.
It is a fatal objection to the jurisdiction of the court when it has not cognizance of the subject-matter of the action, as in the Railway Labor Act, where congress specifically designated the System Board of Adjustment to hear complaints about the interpretation of the agreemnt between the parties, like the Ttransition Agreement.
Remember, the company filed its action prior to the issuance of the mandate and the final dimisal of Addington. They are now referencing a case that doesn't exist, and a decision from the appeals that doesen't help them clarify this non existant case. There is no active controversy between the parties pending in the courts. There is only the company's request clarify a case which no longer exists. The court has no specific authority to decide the case anyway under the definition of subject matter jurisdiction and the Railway Labor Act.
Judge Silver will likely dismiss.