According to the article, on December 31, 2017, congress enacted Internal Revenue Code (IRC) Section 512(a)(7), requiring nonprofits to pay a 21 percent unrelated business income tax (UBIT) on qualified transportation benefits provided to employees. But the Taxpayer Certainty and Disaster Tax Relief Act of 2019 retroactively repealed Section 512(a)(7), which enables nonprofits to get refunds for taxes paid under the rule. On January 21, the IRS issued guidance on how nonprofits should request refunds on taxes paid under the now-defunct rule.
Regarding 2019, some nonprofits may have also paid estimated taxes under the repealed rule. Venable had some advice: "Nonprofits that paid estimated taxes in 2019 based on Section 512(a)(7) might have to wait until they file their Form 990-T for 2019 to claim a refund of the estimated tax paid unless the IRS begins automatically generating these refunds".