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Governor Charlie Baker on Thursday appointed Thomas Quinn the permanent Bristol County district attorney but rejected complaints that he had in any way jeopardized the prosecution of former NFL star Aaron Hernandez’s murder trial when he rescinded a host of last-minute Patrick administration appointments.

Quinn was appointed district attorney by former governor Deval Patrick in the closing days of Patrick’s tenure, and he took office Jan. 2. But last Friday, Baker canceled Patrick’s last-minute appointments, and Secretary of State William F. Galvin argued that the list of rescissions included Quinn — even if Baker hadn’t intended it.

The confusion raised questions among some legal analysts about whether Quinn had legal authority to continue his work.

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With potential complications looming most of this week, Baker’s office released a statement late Thursday saying the governor had made Quinn’s appointment permanent. Baker’s spokesman, Tim Buckley, insisted the appointment was not a recognition that Galvin’s position was correct.

“Both the Patrick administration, the appointing authority, and Governor Baker maintain that Mr. Quinn was serving in an ‘acting’ capacity, and as such was not subjected to Governor Baker’s order to rescind some recent appointments,” Buckley said.

Galvin said it made no difference whether Quinn was designated as “acting” district attorney in terms of the statute that allows for a governor to withdraw an appointment two weeks after it is made. He said he was glad to see the legal standoff between him and the Baker administration resolved.

“I am anxious to remove all doubt about these appointments and see resolution,” Galvin said.

Whether Quinn’s authority over the past several days could — or would — still be challenged was uncertain Thursday.

John Amabile, a criminal defense lawyer in Brockton, said that if defense attorneys were seeking a stay of prosecution because of the uncertainty in the district attorney’s office, they would have had a better chance at success if they had acted between the time Quinn’s appointment was apparently rescinded and the time he was appointed by Baker.

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“Going back retroactively is going to be less effective. At the very least, you have to show there was some harm to the case” by arguing that there wasn’t a properly appointed district attorney in charge, Amabile said.

Defense attorneys for Aaron Hernandez did not bring up the matter at a jury selection hearing in Bristol Superior Court Thursday. And Gregg Miliote, spokesman for Quinn, said no defense attorneys have filed complaints or motions related to the matter in Bristol courts.

Appearing earlier Thursday on WGBH-FM’s “Boston Public Radio,” Baker insisted that his actions in no way created potential legal complications in the nationally watched Hernandez case. Jury selection in the case began this week.

“It won’t affect the Hernandez trial in Bristol County, I can promise you that,” Baker told a caller to the program who had asked him about the issue.

“Governor Patrick believed his appointment of Tom Quinn was an ‘acting’ appointment, and so do we,” Baker said in his appearance on the show hosted by Margery Eagan and Jim Braude. Baker was appearing on the program’s monthly “Ask the Governor” segment.

In his announcement of the appointment, Baker praised Quinn as an “experienced manager with a solid record that fully qualifies him for the position of district attorney and I am pleased to announce his appointment to this important post.”

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And in a written statement, Quinn said he was grateful for Baker’s confidence in him. “I look forward to working with the Baker-Polito administration to make the administration of justice more efficient and effective,” he said. “I would especially like to thank my fellow employees at the district attorney’s office for their strong and touching support.”

When he appointed Quinn, Patrick also ordered a special election for the seat, set for 2016. The seat became vacant when Sam Sutter resigned after he was elected Fall River mayor in December. He had won another four-year term as district attorney in the November general election.

In his radio appearance, Baker said he had sent the unusual one-sentence letter rescinding all of Patrick’s appointments since Christmas because of time constraints. No other governor in recent memory had made such blanket recisions.

The usual notice provides specific names and positions.

Baker said his administration, facing a tight deadline, could not locate the names and positions of all those who had been appointed to boards and commissions.

“We were stuck in kind of a tough spot, no documentation, no knowledge, very little information shortly after we took office with respect to who actually had been appointed during that final frenzy,” Baker said.

“And rather than lose the three or four days it was going to take before people could give us access to some of the information that had been archived, we wrote a very simple one-line note that said if somebody had been appointed in the recent 15-day period, then that appointment was rescinded,” he said.

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Frank Phillips can be reached at phillips@globe.com.