It was the hectic week before Thanksgiving, and Amrith Kaur — the legal director of an advocacy group called the Sikh Coalition — was not prepared for a surprise update from the Equal Employment Opportunity Commission that could have dramatic consequences for her clients.

With little warning, the EEOC published a 112-page overhaul of its guidance on religious discrimination in the workplace. The feedback period was proceeding with no time to spare — she would have to file any comments by Dec. 17.

“To my knowledge, that was the first time that pretty much everybody heard about it,” said Kaur, who was busy handling home schooling for her children, ages 8 and 10, when the announcement popped up. “There’s so much happening, and I think it’s very strategic the way this was brought out.”

The guidance is among scores of last-minute actions that ProPublica is tracking on their way through the approval process, many of them accelerating as it became clear that President Donald Trump’s time in office would end on Jan. 20.

The EEOC’s guidance explains the complicated statutes and legal precedent that govern how employers must deal with religious freedom issues in the workplace. It doesn’t have the force of law, but it can be cited in lawsuits, and it serves as a manual for managers navigating thorny situations.

As she dug into the document’s dense language and footnotes, Kaur was particularly distressed because of what she found to be a slant toward large Christian employers like colleges and social service agencies, rather than smaller religions like Sikhism, which face widespread prejudice. For example, in recent days, she’s had to focus on advising health care workers who keep long beards as part of their religious practice. Some hospitals and nursing homes ban facial hair to ensure a proper fit for face masks, but Kaur has been able to work out accommodations that are both COVID-19-safe and allow medical staff to observe their faith — which the new guidance doesn’t address.

As the comment period ended, dozens of other civil rights groups and Democratic leaders filed letters appealing for more time and agreeing that the new guidance could allow for more discrimination under the guise of religious freedom, rather than less.

Unlike many midnight regulations that President-elect Joe Biden could roll back, the EEOC commissioners have multiyear terms, so the Biden administration won’t be able to change the board’s composition until 2022. Meanwhile, Kaur fears that adverse case law could accumulate. “It is our belief that these proposed changes in the manual, and what I think is a clear bias towards Christian viewpoints at the expense of all others, it’s just going to have profound negative effects for years to come,” she said.

Most administrations kick rule-making into high gear once they know their party is leaving the White House, and Trump’s is no exception. A flood of new entries in the Federal Register includes several rules and guidance documents that widen lanes for religious institutions to exclude those who do not share their faith, or narrow the options for beneficiaries of federal programs who feel uncomfortable receiving services in a religious context.

Some of the freshly finalized rules codify an executive order that Trump issued in 2018 declaring that faith-based organizations should have full access to government grant programs without having to modify their operations. They deliver on the promises that Trump made to evangelical Christians during his presidential run, and which he and Vice President Mike Pence campaigned on again in 2020 — the White House’s website contains 228 mentions of “religious freedom,” in posted speeches, press releases and other official statements.

Earlier in the term, Trump’s religious freedom agenda focused on the Department of Health and Human Services, which adopted a rule that protects health care providers who object to certain procedures — namely abortion — on religious grounds, among a host of other actions. Even now, HHS is witholding funds from states that require their insurance plans to cover abortion.

Later, Trump moved on to further integrating religious organizations into the operations of government itself.

In an October interview with the Religion News Service, Trump touted his administration’s work to install religious freedom liaisons in every Cabinet agency. “Led by Pastor Paula White, this Initiative is working to remove barriers which have unfairly prevented faith based organizations from working with or receiving funding from the federal government,” Trump said in a written Q&A.

On that front, the first big change finalized Dec. 7 was at the Office of Federal Contract Compliance Programs, an agency within the Labor Department that enforces compliance with civil rights laws among recipients of federal dollars. The new rule clarifies that private companies can qualify as “religious employers” under certain conditions, and that religious employers may deny positions to people who do not subscribe and adhere to their faith. That could include not hiring people in same-sex relationships or someone of a different religion.

Advocates for marginalized communities say that the rules open the door for religious institutions to use faith as a pretext for firing or simply declining to hire people whom they would prefer not to employ because of other factors — such as sexual orientation or medical disability — even though discriminating on those bases is still illegal.

“If that employer just throws up their hands and says ‘RFRA!’ it’s like a get out of jail free card,” said Human Rights Campaign legal director Sarah Warbelow, referring to the Religious Freedom Restoration Act, a 1993 law that strengthened the test for what can be considered a burden on the free exercise of religion.

Religious employers say that situation likely won’t occur often, but they still supported the change. Jamison Coppola, legislative director of the American Association of Christian Schools, said that most people who work for his member institutions accept that abiding by faith-based principles is part of the deal.

“It’s a rare occurrence where people enter an employment decision and then realize, ‘Oh, I guess we have some difference of opinion about this,’” Coppola said. “I just think that we don’t run into it that often, because of how we approach the totality of what we’re trying to do as an assembly of believers.”

Among the largest supporters of the rule was Catholic Charities, which, according to USAspending.gov, received approximately $189 million in federal contracts and grants in 2020 across all of its affiliated organizations.

The second change, finalized a few days later after a lightning-fast trip through the Office of Management and Budget, was a joint effort of nine agencies that elaborated on the religious freedom exemptions for recipients of their own spending. It gets rid of the earlier requirement that religious providers of federally funded social services, from food banks to job training, provide referrals to secular alternatives. In the case of “indirect” aid that travels with the beneficiary, like child care and housing vouchers, it eliminates the requirement that there must be a secular option available.

The concerns with those rules center around the possible exclusion of people who may feel uncomfortable getting aid in an explicitly religious setting, even if providers are not allowed to proselytize as part of the programming.

“They are really putting what they believe are the interests of these large social service providers ahead of the people who receive the service,” said Maggie Garrett, vice president of public policy at Americans United for Separation of Church and State. “Their priority is not the LGBTQ youth who is seeking services because they were kicked out of their home.”

Not all religious organizations — or even Christian organizations — support the changes. Some have recommended that the requirements for secular alternatives be kept because of the delicate political balancing that has gone into these rules over the years.

“It eased peoples’ conscience or concerns about having more faith-based groups be involved in these services,” said Stanley Carlson-Thies, founder and senior director of the Institutional Religious Freedom Alliance, which represents Christian employers. Now, he fears a backlash.

“I personally don’t know of anybody who was asking for this change, but there it is, and I don’t think it’s a good change,” Carlson-Thies said. “And I think that one thing that’s going to happen is that the next administration is going to go through a regulatory process and take those out, and they’ll do other things too that to my mind won’t be so positive.”

Finally, the Trump administration is moving forward with its guidance for all employers, whether they contract with the federal government or not, through the EEOC.

The last time the agency updated its religious freedom guidance, in 2008, it went through an expansive, yearslong process that incorporated feedback from a panoply of groups that represent faith communities and those impacted by them, such as advocates for LGBTQ people and women’s reproductive rights.

Trump’s EEOC has shifted its emphasis toward supporting the rights of religious employers and employees. For example, it took up the case of two Kroger employees who were fired after they objected to wearing a rainbow heart emblem on their uniforms, which they interpreted as a symbol of support for gay rights.

In a November online forum hosted by the conservative Federalist Society, EEOC General Counsel Sharon Fast Gustafson articulated the new focus. “The EEOC has an interest in the courts getting all aspects of employment discrimination right, whether getting it right helps the employee, or whether getting it right helps the employer,” she said. “Religious liberty has been a high priority for the current administration, where everyone I have spoken with has been unequivocally supportive of religious liberty for all.”

However, many religious groups felt left out of the process that led to the EEOC’s new guidance.

The updates were put together in the wake of a landmark Supreme Court decision in June that declared gender identity and sexual orientation to be protected classes in an employment context, making it much more difficult to discriminate against gay, lesbian or transgender people in the workplace. EEOC spokeswoman Christine Nazer said the new guidance was drafted by the agency’s office of legal counsel, with no input from external stakeholders.

Many groups that closely track religious freedom issues found out about the updates during a three-day listening session convened by the commission’s Religious Freedom Work Group, which is led by Assistant General Counsel Christine Lambrou Johnson. According to her LinkedIn profile, Lambrou Johnson is a member of the Christian Legal Society, which describes itself as “a fellowship of Christians dedicated to serving Jesus Christ through the practice and study of law, the defense of religious freedom and life, and the provision of legal aid to the needy.”

Nazer said the Religious Freedom Work Group’s duties are separate from the development of the guidance, and that the commission voted to publish the guidance for public comment on Nov. 9, giving additional time for discussion. But at that meeting, the body’s two Democratic commissioners said that they hadn’t had enough time to provide input or that it was rejected by the commission’s Republican members. The Democratic commissioners also raised questions about the legal soundness of some of the guidance’s interpretations and pleaded for the vote to be delayed. It wasn’t.

In addition to liberally interpreting exemptions from Title VII of the Civil Rights Act for religious employers to hire and fire on religious grounds, the guidance also raises the bar for intervention when one employee might be harassing another on religious grounds. And it says little about some of the common questions raised by the COVID-19 pandemic, such as the Sikh nurses that Kaur has been helping negotiate accommodations with hospitals, which would be easier if the EEOC had set out a clear position.

In response to these concerns, Nazer said that the commission is “carefully considering all of the comments provided to us by our stakeholders as we finalize the guidance.”

Kaur is not comforted.

“Manuals like this, that are sort of taken as law even though they’re not, are what our government is going to rely on to make a decision on whether discrimination took place,” Kaur said. “We have the Title VII protections in the Civil Rights Act for a reason, and to try and decimate it in a way that’s not supported by the law is a sad and disappointing attempt at getting around having to be fair to everybody.”