A full shutdown of the federal courts in Connecticut was averted when Congress reached a deal to get the government running again, but no federal judicial agency was left completely unscathed.

Connecticut’s Acting U.S. Attorney Dierdre Daly said there were some delays in ongoing criminal investigations, as a handful of wiretapping operations were suspended and law enforcement personnel pulled off duty. Other delays “resulted from the fact we were not operating at full speed. Most of the support staff were furloughed, so even though the assistant U.S. attorneys were here, things were not proceeding as quickly as they typically are.”

Likewise, some civil cases in the U.S. District Courts were delayed by court-appointed lawyers, who were concerned they might not get paid for work done while the shutdown was underway.

When the budget deal was approved by Congress late on October 16, reopening the government, Daly, along with the federal judiciary, breathed a collective sigh of relief.

In Connecticut and elsewhere, reserve funds, made up of collected federal court fees, ensured the judiciary would be fully funded for the first two weeks of the shutdown. But almost immediately after the congressional impasse started October 1, there was talk of suspending some court services.

Last week, before the shutdown ended, Chief U.S. District Court Judge Janet Hall, who oversees the federal courthouses in New Haven, Bridgeport and Hartford, was contemplating which “non-essential workers” to send home. And in a notice that was posted on the court’s website, Clerk Robin T. Tabora informed prospective jurors that their payments might be delayed.

At the U.S. Bankruptcy Court in Bridgeport, where cases typically move at a slower pace than civil matters in other federal courts, clerk Gary M. Gfeller said he and the judges had started to look at ways to keep the court running after the fee reserves had run out. Although operations were never affected, Gfeller said he started to review what chores could be set aside until the shutdown ended. For example, some human resources functions, such as administration of benefits or employee reviews could have been delayed, he said. “But that didn’t happen.”

However, lawyers who practice before Connecticut’s immigration courts say that operations were suspended during the government shutdown, delaying hearings and putting the status of some immigrants in limbo. Court officials did not return messages requesting comment late last week.

The deal approved by Congress to raise the debt ceiling provided $51 million in additional funding to the judiciary and to federal defenders. But some federal court officials said the gain was small compared to the $350 million in budget cuts already made earlier this year as a part of sequestration.

Connecticut Federal Defender Terence S. Ward, whose office provides legal representation for indigent defendants in criminal cases, had a bittersweet reaction to last week’s budget deal. “Luckily, the shutdown ended before the funds the court system was operating on ran out,” he said, adding the shutdown ended day before his office would have faced the possibility of keeping lawyers home.

But, he added, the congressional agreement does not solve his long-term funding woes. “For us, the sequester is a bigger problem than the shutdown,” he said, “We still have the sequester cuts to deal with under the Budget Control Act for the next several years…

Earlier in the week, he shared his concerns, in spite of the shutdown ending.

“We’ve already been told we may have to reduce our budgets by 23 percent for fiscal year 2014,” said Ward, who became the state’s federal public defender last year. “My budget has virtually no discretionary funds.”

Even with the shutdown over, his staff faces potential salary cuts. He’s already been forced to take their cell phones away. With six lawyers, down from seven last year because of the April retirement of Ronald Resetarits, Ward is concerned that services will be impacted. At the end of the year, another longtime lawyer in the office, Gary Weinberger is retiring. With a hiring freeze in place, the empty spots probably won’t be filled.

At the U.S. Attorney’s Office, Daly said she, too, is concerned about the sequester cuts, which she said has created a greater “overall impact” than the shutdown.

“We’ve been under a hiring freeze for three years,” she said, “and were also living under the sequestration cuts that have kicked in for fiscal year 2014. We anticipate a number of unpaid furlough days, so that was all in the context under which our employees were living when the shutdown occurred. It’s been a difficult slog going forward.”

In spite of a financial climate that might be considered “demoralizing” for workers, Daly said her office “managed as well as we possibly could.”

Daly said she was forced to furlough about 40 employees during the shutdown, including civil lawyers, support staffers and the office’s public information officer. Still, the staff pulled together to get necessary work done.

“We managed as well as we possibly could,” she said. “I’m not sure what is gained by all of this, when you have two categories of employees: those who are told they are non-essential and kept home, and those who are kept at work and not paid. We did try a number of things in terms of addressing morale.”

For instance, she said, the office tried to rotate schedules of furloughed employees, to limit paycheck impacts as much as possible.

“There’s no question, this is very challenging for employees,” she said.•