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EXCLUSIVE: The U.S. Navy quietly rolled back an order punishing SEALs who remain unvaccinated due to their religious beliefs, according to recent court documents.

The order, "Trident Order #12," disqualified SEALs seeking religious exemptions from the COVID-19 vaccine from training, traveling for deployment and conducting other standard business. It was first issued on Sept. 24, 2021 by Rear Admiral H. W. Howard, the former commander of Naval Special Warfare Command, and all special warfare forces were initially expected to come into compliance with the vaccine mandate by mid-October 2021.

The order specifically said that "Special Operations Designated Personnel (SEAL and SWCC) refusing to receive recommended vaccines based solely on personal or religious beliefs will still be medically disqualified." In addition, unvaccinated SEALs seeking religious accommodations would have to fill out a separate waiver to remain deployable.

The order was put on hold due to a preliminary injunction issued by the Fifth Circuit Court of Appeals in early 2022 as part of an ongoing lawsuit brought by First Liberty Institute and Hacker Stephens LLP on behalf of 35 active-duty SEALs and three reservists seeking a religious exemption to the mandate.

However, according to a new filing in the lawsuit, the Navy quietly rolled back Trident Order #12 on May 22, 2022, a few months after the injunction was issued. 

NAVY SEALS SEEKING RELIGIOUS EXEMPTIONS TO VACCINE MANDATE FACING INTIMIDATION AND HARASSMENT, SOURCES SAY

Navy SEALs vaccine mandate

Members of the Special Operations Team of the Cypriot National Guard and U.S. Navy SEALs participate in a joint military training in Limassol, Cyprus, September 10, 2021. REUTERS/Yiannis Kourtoglou

A communication order was circulated by the Navy on May 23 with the subject: "NSWC CLOSEOUT TO TRIDENT ORDER #12 - MANDATORY VACCINATION FOR COVID-19." NSWC refers to the Naval Special Warfare Command.

"This order rescinds reference A," it states, referring to "Ref A" as "Trident Order #12 on COVID-19 Vaccinations."

The May 23 communication order also said Navy commands "will continue to follow guidance, as appropriate, regarding COVID-19 vaccination, accommodation requests, and mitigation measures."

It is not immediately clear whether the Navy replaced the order with any other document or the reasoning behind Trident Order #12's termination. The Navy spokesperson told Fox News Digital, "The Navy does not comment on ongoing litigation."

According to a filing from plaintiff attorney Heather Gebelin Hacker to a Fifth Circuit clerk, the legal team representing the SEALs only became aware of the recession of the order on Sept. 1, months after it was rolled back.

"To the best of counsel’s knowledge, Trident Order #12 was not replaced. As the Court will recall, Trident Order #12 stated that SEALs who are unvaccinated due to religious beliefs are medically disqualified, though SEALs who are unvaccinated due to medical reasons are not automatically disqualified. Trident Order #12 also implemented the COVID-19 vaccine mandate at the command level for Naval Special Warfare forces, setting a deadline of compliance for October 17, 2021," the SEALs' legal team wrote.

U.S. Navy SEAL candidates participating in "surf immersion" during Basic Underwater Demolition/SEAL training at the Naval Special Warfare Center in Coronado, California, May 4, 2020. U.S. Navy SEALs are undergoing a major transition to improve leadership and expand their commando capabilities. (MC1 Anthony Walker/U.S. Navy via AP)

U.S. Navy SEAL candidates participating in "surf immersion" during Basic Underwater Demolition/SEAL training at the Naval Special Warfare Center in Coronado, California, May 4, 2020. U.S. Navy SEALs are undergoing a major transition to improve leadership and expand their commando capabilities. (MC1 Anthony Walker/U.S. Navy via AP)

"A copy of the order rescinding Trident Order #12 is attached to this letter. The rescission of Trident Order # 12 does not appear to affect the applicability of Navy or DoD-wide vaccine policies to NSW personnel—it just appears to remove the command-level direction," Hackeron continued.

The lawsuit representing unvaccinated SEALs, first reported by Fox News Digital in November, has since been amended to extend to a class action lawsuit encompassing all Navy service members seeking religious accommodation.

ADMIRAL WHO SAID UNVAXXED SEALS CAUSE 'IMMEDIATE HARM' TO NAVY ADMITTED NO COMBAT OPERATIONS AFFECTED

First Liberty's Senior Counsel and Director of Military Affairs Mike Berry told Fox News Digital, "Now that the Navy has rescinded this unlawful order, the only reason it won't allow our SEALs to get back to doing their jobs is because of their religious beliefs."

Covid Vaccine Injection

A health worker administers a dose of COVID-19 vaccine during a vaccination clinic in Reading, Pennsylvania. (AP Photo/Matt Rourke, File) (AP)

"America faces many national security threats, and the Navy is suffering a historic recruiting crisis. There's no good reason to keep these trained and experienced warriors from serving," Berry said.

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In addition, during a recent deposition, William Lescher, the former vice chief of naval operations, stated he was "unaware" of any Navy SEAL combat missions that had been negatively affected by COVID-19, despite his earlier claim that the vaccine mandate was necessary for successful Navy operations.

In a sworn affidavit before the Supreme Court earlier this year, he stated that allowing unvaccinated SEALs will cause "immediate harm to the Navy" and "to the national security of the United States" and could be considered a "dereliction of duty."