Almost two years ago, the U.S. Food and Drug Administration’s ability to use a controversial report on menthol cigarettes nearly disappeared like a puff of smoke.

In a Washington federal district court, Judge Richard Leon found that three members of the scientific advisory committee responsible for the report had conflicts of interest against the tobacco industry. He ordered that the three members be removed over their financial relationships with pharmaceutical companies and their history of giving expert testimony against tobacco manufacturers. And he barred the government from using the report, handing a victory to two major tobacco companies that were challenging the FDA’s Tobacco Products Scientific Advisory Committee.

As a Justice Department lawyer would later write, the July 2014 ruling was a “ unique judicial venture” into an area typically left to an agency’s discretion—the handling of a conflict of interest or the appearance of one.

But this month, the U.S. Court of Appeals for the D.C. Circuit overturned Leon’s order, finding that R.J. Reynolds Tobacco Co. and Lorillard Tobacco Co.’s alleged injuries “are too remote and uncertain” for the two to have standing in the case. The decision lifted the injunction on the FDA’s use of the menthol report.

In a patch of largely unfamiliar legal territory, the decision also clarified that a claim against an advisory committee should come after an agency’s final action.

But the ruling otherwise raises questions—and risks—for both sides.

The FDA was required to create the Tobacco Products Scientific Advisory Committee under the 2009 law that empowered the agency to regulate the tobacco industry. The committee’s first order of business was to report on how menthol cigarettes were affecting public health.

For the tobacco industry, the stakes were high. The report, approved unanimously by the committee’s nine voting members, advised that “removal of menthol cigarettes from the marketplace would benefit public health in the United States.” The companies alleged that the three members’ financial interests created a heightened risk of adverse regulations on menthol tobacco products, but the D.C. Circuit noted that “it remains unclear whether the FDA will issue a final rule, and what it would say.”

“Ripeness concerns underscore this point: part of the reason the injury is too remote is that, if the FDA chooses not to issue a rule, this case ‘may not require adjudication at all,’ ” wrote Circuit Senior Judge Stephen Williams.

But the opinion was silent on what a plaintiff must prove, even after showing that a committee is tainted, to have an agency’s action thrown out.

“That’s the $100 million question in this case for the tobacco companies,” said Scott Nelson, an attorney at the Washington-based Public Citizen Litigation Group, who filed an amicus brief supporting the government in district court. (The brief was filed on behalf of the American Heart Association, the American Cancer Society and other public health groups.)