Here's the Thing
What I think is interesting about this case is that it really turns, for all intents and purposes, on the Federal Register Notice. The Court treats the Notice as if it has the full force and effect of law. If the notice was an amendment to a regulation (rather than an informational notice) it might, I honestly don't know off the top of my head. On the other hand, it seems that the protest got to Customs (in the larger sense) in a timely manner. While the importers (and everyone else) are presumed to know the contents of the Federal Register, can "Customs" be presumed know to that it received a protest at another port? If Customs sent a letter to the main corporate address of a large company, would the Court find that the company's counsel or compliance manager should have known about the letter?
Regardless of the law (which is a funny thing for a lawyer to say), this looks to me to be one of those maddening situations in which someone at Customs might have asked why the agency was litigating this issue. If the drawback claim was valid but for the irregularities of the filing and there was some justifiable confusion surrounding the change in responsible offices, couldn't anyone simply say, "Grant the claim. The company should be able to get the drawback to which it is entitled?" I get that equity basically does not compel the U.S. government to do anything. I am not talking about equity (or law), I am talking about trade facilitation, management, and goodwill.
Just a thought.
On the equity front, in United States v. Canex Int'l, the Court of International Trade did use equity to find that the United States is entitled to prejudgment interest in a penalty case. According to the Court, "It would be inequitable and unfair for the government to make an interest-free loan of this sum" from the date of a demand for liquidated damages. In this case, the Court said that "[E]quity compels the court to grant prejudgment interest."