Under rules issued in 2017, the Trump administration expanded exemptions from the contraceptive coverage mandate, allowing employers to opt out if they had religious or moral objections. Judge Wendy Beetlestone of the Federal District Court in Philadelphia blocked the administration in December, saying the Affordable Care Act did not authorize such “sweeping exemptions.”

Judge Haywood S. Gilliam Jr. of the Federal District Court in Oakland, Calif., blocked the rules a week later. For a substantial number of women, he said, the rules would “transform contraceptive coverage from a legal entitlement to an essentially gratuitous benefit wholly subject to their employer’s discretion.”

Under the 2017 rules, he said, “more employers than ever before are eligible for the exemption.”

The Trump administration has appealed both decisions. And the new rules are unlikely to end the legal fight over contraceptive coverage, which has been raging in courts around the country for more than six years.

The Little Sisters of the Poor, an order of Roman Catholic nuns, told the United States Court of Appeals for the Ninth Circuit, in San Francisco, last week that it should rule on the critical legal questions in the case “even if and when the agencies issue yet another version of their rule.”

Among those questions is whether the religious exemption is legal or whether it violates provisions of the Constitution barring the establishment of religion and guaranteeing equal protection of the laws.

Mr. Trump’s efforts to roll back the contraceptive coverage mandate were inspired, in part, by the Little Sisters. “I will make absolutely certain religious orders like the Little Sisters of Poor are not bullied by the federal government because of their religious beliefs,” he said a month before the 2016 election.

One challenge to the Trump administration rules was filed by the State of California, joined by Delaware, Maryland, New York and Virginia. The other was filed by Pennsylvania.