The VA blundered its first public act of accountability in this year’s wait list scandal, with department investigators and attorneys failing to make a case stick against the Phoenix clinic director who oversaw the cooked books and secret lists that left veterans struggling for care.

Sharon Helman, the director, was fired from the Department of Veterans Affairs, but only because she improperly took thousands of dollars in gifts. A personnel appeals judge last week rejected the VA’s claim that she should also have been dismissed for overseeing the wait lists.

Ms. Helman’s case is just one that the VA is handling in the wake of the wait list scandal, and so far its investigators have had about 20 percent of their decisions weakened or overturned on appeal, according to the House Veterans’ Affairs Committee.

Now top lawmakers on Capitol Hill and independent analysts are questioning how VA investigators failed to make the wait list scandal stick to Ms. Helman, who became its central figure.

Cheri Cannon, a lawyer at Tully Rinckey PLLC, said VA investigators interviewed witnesses without putting them under oath, and VA attorneys erred in charging Ms. Helman with being directly connected to the wait lists. They should have charged her with mismanagement or not knowing what her employees were doing, Ms. Cannon said.

“The agency blew this, in my view; the agency charged her wrong,” she said. “That being said, they charged her with this other stuff [ethics violations for gifts]. They knew they had a weak case going in. Otherwise, why do it?”

Employees who are fired are able to appeal the termination to the Merit Systems Protection Board. A law passed over the summer requires an administrative law judge to make a final decision on the appeal within 21 days. The old system could take more than a year and included a second appeals process that is now gone.

Stephen Mish, the administrative judge who heard Ms. Helman’s appeal, ruled that her firing was appropriate because she had accepted thousands of dollars in inappropriate gifts, including tickets to hear singer Beyonce and an $11,000 trip to Disney World.

But the judge said the VA did not prove its case that Ms. Helman was connected to the secret lists, which kept veterans waiting weeks or months for care. A whistleblower charged that veterans died because they were stuck on those lists — a claim the VA’s inspector general said was possible but could not conclusively prove.

The judge mocked the VA’s case, including pointing out that VA attorneys claimed she created a hostile work environment at the Phoenix facility — nine months before she began her job there.

The judge wrote in a footnote that examples like this only help Ms. Helman’s argument that her firing was part of the agency’s “win-at-all-costs railroading campaign” against her. The judge wrote that he assumed the VA’s errors “were inadvertent.”

Rep. Jeff Miller, Florida Republican and chairman of the House Committee on Veterans’ Affairs, said the judge’s ruling showed something went wrong, either with the VA’s case or with the administrative judge, who could have “used a little more common sense.”

“While I am glad the MSPB upheld Sharon Helman’s firing, the fact that the ruling did not connect the central figure of VA’s wait time scandal to any wait time schemes demonstrates a huge problem with the way this case was handled,” Mr. Miller said. “This issue is something our committee will study in detail next Congress in order to help maximize the department’s ability to get rid of corrupt and reckless managers in the future.”

Ms. Cannon said the VA likely still sees the ruling as a victory since Ms. Helman is now permanently off the payroll.

“A victory is a victory,” she said. “Do they probably wish they’d won on some of the charges related to the scandal? Yes. Are they still done with an employee who obviously violated ethics rules pretty flagrantly? Yes, that’s seen as a victory.”

Ms. Helman’s is one of 40 cases of proposed or completed punishment related to the wait time scandal that an appeals board has upheld since June. Another six cases saw a lesser punishment, and another six were overturned, a House Committee on Veterans’ Affairs staff member said.

The VA, in a statement, said it tried to follow lawmakers’ wishes in making its case against Ms. Helman, and said it is trying to improve care after the scandal.

“We are making progress in improving access to care at Phoenix and VA facilities nationwide, and we are pleased that MSPB’s decision helps us begin to put the leadership failures at Phoenix behind us,” the spokesman said.

Ms. Helman may still face criminal charges for her ethics violations. Cathy Gromek, a spokeswoman for the VA Inspector General, said investigators are continuing to work with the FBI on a criminal investigation.

New VA Secretary Robert McDonald promised to clean up the agency and impose accountability, though he has clashed with members of Congress who say he should have moved quicker to fire people and was giving them too many opportunities to fight their dismissals.

Some lawmakers questioned the VA’s decision to give employees a five-day notice before taking any disciplinary action. Mr. Miller and others in Congress have said it adds more red tape to a firing process lawmakers were trying to simplify and gives employees a chance to retire before they can be fired.

But lawyers, including Ms. Cannon, have said the five-day rule is arbitrary and should be longer. Most other federal agencies give employees 30 days to respond to charges.

The chief administrative judge in Ms. Helman’s case said five days was plenty of time since she had been on administrative leave and knew of the proposed discipline for five months. But he left the door open for others to question if both the five-day notice and the requirement to decide appeals within 21 days afforded adequate due process rights.

“The shortened process of 38 USC 713 is new,” he wrote in the decision. “Expecting the agency to accomplish in a few days what normally requires several weeks or more to do correctly is simply not realistic.”

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