By Marshall Cohen, CNN

(CNN) — President-elect Donald Trump hasn’t been sworn in yet, but his looming return has already upended hundreds of pending prosecutions against his supporters who attacked the US Capitol on January 6, 2021, and has disrupted the ongoing effort to arrest more rioters.

The historic effort by Justice Department prosecutors and FBI agents to investigate the deadly Trump-inspired storming of the Capitol has led to more than 1,570 arrests in nearly all 50 states, making it the largest criminal probe in American history. New arrests are slowly still trickling in, four years later, including recent cases against a member of the Proud Boys and a rioter who tried to stab police with a flagpole.

But the political reality has already tanked morale inside the Justice Department division that handles these cases — and is hampering efforts to secure guilty pleas in about 300 pending cases, as defendants balk at negotiations, according to a federal law enforcement official involved in the sprawling investigation.

The official also said investigators have decided to use their limited time and resources to go after January 6 fugitives suspected of attacking police, meaning lower-level rioters who breached the Capitol but didn’t contribute to the violence will likely never be charged or held accountable.

Much — if not all — of that work will likely be undone once Trump assumes power later this month and fulfills his campaign promise to grant presidential pardons to Capitol rioters.

“Sometimes, it feels like rearranging the deck chairs on the Titanic,” the official said.

Plea talks frozen

The vast majority of federal criminal cases are resolved with plea deals, and that has been true for the January 6 cases. As of last month, about 1,250 of the 1,570 Capitol riot prosecutions had already been adjudicated, and 80% ended with a guilty plea.

For the roughly 300 cases still active and unresolved, Trump’s electoral victory essentially froze all of the plea negotiations that were ongoing, the official said.

“What defense attorney would plead their client out right now?” the official said.

One lawyer who represents many January 6 defendants told CNN that the defense strategy has indeed shifted. Rioters are excited by the election results, clamoring about pardons, and aren’t eager to cut any deals with prosecutors. Instead, they’re seeking to delay court proceedings until after Trump takes office. Some defendants have even publicly lashed out in court against judges and prosecutors, invoking Trump’s pardon pledge.

Instead of haggling with prosecutors, the defense attorney said many of the January 6 lawyers are spending their time figuring out how to get their clients on any eventual pardon list — if Trump decides to grant clemency on a case-by-case basis, as he said he’ll do.

Prioritizing felony cases

After the election, the FBI circulated guidance in an internal memo indicating that the investigation would continue but will focus on people suspected of committing felonies, especially if they assaulted police officers, the federal law enforcement official told CNN.

This is consistent with the recent pace of the investigation, which has largely prioritized felony cases. In earlier phases, prosecutors charged hundreds of misdemeanor-only cases against people who breached the Capitol but never attacked anyone or broke anything.

As a result of this guidance, many of the trespassing cases will now go unprosecuted.

“In a very real and practical way, agents and prosecutors have to consider whether it’s the right expenditure of resources, and whether it’s ethically sound, to go forward with a prosecution if there’s a good chance it’s going to be stopped by the president,” said former FBI Deputy Director Andrew McCabe, who is now CNN’s senior law enforcement analyst.

Arrests are still trickling in, slowly, with about a dozen new cases since the election.

Prosecutors recently charged a Texas man who allegedly smashed the shutters on a Capitol window, an Alabama man who allegedly tried to stab police officers with a flagpole, a North Carolina woman who breached the Senate gallery, and a member of the right-wing Proud Boys group from New York, according to court filings. They all face felony charges.

‘Morale took a hit’

It’s difficult to fully capture the scope of the federal January 6 investigation. Hundreds of federal law enforcement officials have been involved in the exhaustive four-year effort. It’s so big that the FBI is still working through tips that were submitted days after the attack.

Investigators combed through thousands of hours of security camera and bodycam footage in hopes of identifying individual rioters. They’ve secured thousands of subpoenas and examined massive troves of phone metadata, text messages, geolocation information and social media posts. And each case that gets charged follows a tedious court calendar.

In a statement on Monday that commemorated the January 6 attack, Attorney General Merrick Garland said the probe has been “one of the most complex, and most resource-intensive investigations” in US history. He also said he was “proud” and “grateful” for investigators’ “unrelenting integrity” and “the sacrifices they have made over the last four years.”

This probe is “a massive piece of the institution’s work,” McCabe said. So naturally, with Trump poised to negate much of this legacy through pardons, morale has tanked among some career officials who have been working these cases, the federal official told CNN.

“Agents and prosecutors are never going to get rich or famous — it’s not about having a 401(k) at the end of a career,” McCabe said. “It’s about doing justice day-to-day. The payoff is the satisfaction of living up to the oath that you took, doing something positive for your country, mitigating a threat, and standing up for the fair application of the rule of law.”

While Trump has said he plans to issue pardons on day one, he hasn’t said much about whether he also wants to shut down the January 6 probe itself – which experts say would be a major abuse of power, but within his authority. Though if he goes down that path, he might need to wait until the Senate confirms some of his Justice Department appointees.

“Morale took a hit, but it’s not like we’re going to stop, or like we got any weaker,” the federal law enforcement official told CNN. “In a marathon, you get a cramp. That happens. But that doesn’t mean you quit the race. You power through it, and then you finish strong.”

This story has been updated with a statement from Attorney General Merrick Garland.

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