“From a pure public health perspective, I would say let it go, it’s not worth the fight,” said Dr. Carlos del Rio, an infectious disease specialist at Emory University in Atlanta.

At the same time, it could be difficult for the White House and the C.D.C. director, Dr. Rochelle P. Walensky, to rationalize the decision to appeal the judge’s ruling, given that they have increasingly cast mask wearing as a matter of personal choice. On Tuesday, Mr. Biden himself was noncommittal when asked if people should wear masks on planes, saying that the decision to do so was “up to them.”

Just two months ago, the C.D.C. changed its guidelines in a way that made it far less likely that a county would be considered high risk. Only in high-risk areas does the agency now recommend indoor mask wearing for everyone. It says that those who have immune deficiencies or are otherwise at high risk for severe illness should talk to their health care providers about whether to wear a mask in areas of moderate risk.

Under the new regulations, the C.D.C. said counties should decide the level of risk for their residences based on the number of new Covid-related hospital admissions over the past week, the percentage of hospital beds occupied by Covid-19 patients and the rate of new cases over the past week.

“We want to give people a break from things like mask wearing when these metrics are better,” Dr. Walensky said then. “And then have the ability to reach for them again should things worsen.”

Now cases, though not hospitalizations and deaths, are rising in a majority of states and territories, though the inclines are sharpest in the Northeast and the Midwest. Public health experts say it is up to Dr. Walensky to preserve her agency’s ability to encourage, or even require, mask wearing should BA.2 or another variant, unleash another deadly Covid wave.

“C.D.C. shouldn’t let the drama of this judicial opinion change what it would have done,” said Dr. Celine Gounder, an infectious disease specialist and editor at large for public health at Kaiser Health News. “The important thing is that she is likely to be facing another spike of hospitalizations in the future, another dangerous variant, and she absolutely needs to keep that tool in her pocket — the tool of masking.”

Sharon LaFraniere contributed reporting.