Though the items seized by the U.S. government were shipped to Hobby Lobby, not the museum, scholars say the federal case is a blot on the $500 million museum, which is set to open in November two blocks from Mall over the Federal Center Metro Station in Southwest Washington.

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“They put scholars in a situation where it becomes very ethically difficult for someone to engage in those collections in any way, other than to criticize them,” said Donna Yates, an archaeologist who specializes in the study of antiquities trafficking and art crime. “Are they going to come to the museum, somebody who’s doing significant Biblical research or linguistic research, where they’re going to publish [about] material that’s very likely to be stolen?”

The federal complaint described many layers of suspicion surrounding Hobby Lobby’s purchase of 5,500 artifacts for $1.6 million in 2010: The company never met the dealer, and wired payments to seven different bank accounts. The items arrived in 10 packages at three different Hobby Lobby addresses, labeled only “ceramic tiles” and “clay tiles (sample).”

In a statement, Green said, “We have accepted responsibility and learned a great deal.” Hobby Lobby said that the company made “some regrettable mistakes” because officials didn’t understand the rules for properly bringing antiquities into the country.

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The statement said that the craft store chain — widely associated with its 2014 Supreme Court victory ensuring that devout religious business owners like the Greens do not have to provide coverage for contraception for their employers — started collecting ancient artifacts in 2009. The pursuit of these items was “consistent with the Company’s mission and passion for the Bible,” Hobby Lobby said. The company said it planned to preserve the artifacts and offer them for scholars to study.

That project sounds much like the goal of the Museum of the Bible, where Green has promised to house more than 44,000 Biblical texts and artifacts to lure serious researchers and flashy interactive exhibits to attract tourists.

But for its part, the museum – a nonprofit organization which is not a subsidiary of the craft store company but is led by the same man – said in a statement on Thursday that the artifacts implicated in the federal case were never part of its collection.

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“The Museum of the Bible was not a party to either the investigation or the settlement. None of the artifacts identified in the settlement are part of the Museum’s collection, nor have they ever been. The Museum adheres to the current Association of Art Museum Directors standards on the Acquisition of Archaeological Material and Ancient Art, as well as guidelines set forth by the American Alliance of Museums,” the museum’s statement said.

It also said that the institution “aims to be the most technologically advanced museum in the world.”

Robert Cooley, the vice chairman of the museum’s board, said that the museum’s standards are different from the standards of Green, the chairman.

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“The curators and the director of the collection department have professional standards they go by. The museum does not accept collections without full documented provenance and credibility records,” he said. “Every item in the museum is documented.”

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Numerous other board members and staff members declined to comment on Thursday, directing a reporter to the museum’s public relations representative.

Cooley, the president emeritus of Gordon-Conwell Theological Seminary, is an archaeologist by training himself who has supervised excavations in the Middle East.

“We maintain our standards at the museum. And if any collection, be it the Green family or any other family that donates, does not meet the standards that we require, then we do not take that collection,” he said.

Candida Moss, the co-author of a forthcoming book on the Green family’s rapid acquisition of Biblical antiquities and attempts to promote the influence of Christianity on public life, said that the museum has tried to distance itself from its chairman and his craft stores since the media began reporting on his antiquities acquisitions two years ago.

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“The Greens remain very much involved. Green is still head of the board,” she said. “The fact is, they’re not as separate as they claim. Many of the artifacts will be on loan from the Green collection. There are other items in their collection that scholars are asking questions about.”

Brent Clark, an Oklahoma lawyer also working on a manuscript about the Green family, agreed: “Steve Green is going to be in charge of that thing, come hell or high water.” But Clark doesn’t think the federal case will blunt tourist interest in the museum.

“Keep in mind the Greens are successful merchants to the middle class. They’ve always been marketing silk flowers and fake Christmas trees to the middle class, and it’s made them rich,” he said. “Their instincts tell them that thousands of people are going to get on buses in Cincinnati, Ohio, to go see it, and they’re probably right.”

It’s the university researchers who are most likely to be dissuaded from coming to the museum.

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“Individual scholars will have to ask themselves to what extent are they willing to be complicit,” Moss said.

Yates, the art crime expert, said that many major journals of archaeology research refuse to publish articles based on artifacts whose provenance can’t be proven, and researchers won’t be willing to do work that they can’t publish.

Several scholars, including Yates, said the federal complaint filed Wednesday left them convinced that Hobby Lobby had willfully ignored their own lawyers and other experts, not just that the company had been unaware that they might be importing looted Iraqi goods.

“Basically everyone should be suspicious of any antiquity for sale without a provable history,” Yates said. “Dealers should be telling people that it’s kind of an obvious thing. When we’re talking about Iraq, it’s even more obvious. That this stuff is dodgy, it’s not news…. It’s a known thing in the market. If an object doesn’t have a history that proves that it is legal, you just assume that it is illegal, because it probably is.”

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Joel Baden, Moss’s co-author, said that the Green family’s interest in buying thousands of ancient artifacts likely spurred bad actors in Iraq to steal the items in the first place.

“If Hobby Lobby is willing to buy them, people will be willing to loot for them because there’s a market for them,” he said.

The federal settlement requires Hobby Lobby to send thousands of items back to Iraq. But in many respects, the damage is already done.

“The absolute most important thing for an archaeologist is context. And that’s exactly what these antiquities have lost,” Yates said. “We may not be able to tell if this one came from a whole library, or this was kept in a temple, or they were individual records. We’ve lost absolutely all of that information. All we have are the little tattered remains of what’s written on the tablets.”

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“It’s a huge loss,” she continued, “and all of us could benefit from this information, learning about ourselves and our past.”

Michelle Boorstein contributed to this report.

This story has been updated.