A day after the Orleans Parish Sheriff’s Office finished transferring hundreds of inmates into the city’s new $150 million jail, authorities said Wednesday that they had ironed out some transportation problems that threw a wrench into local court proceedings earlier this week.

But the long-term protocol for shuttling pretrial detainees to and from court remains in flux, and a federal judge summoned Sheriff Marlin Gusman to appear in his chambers next week to discuss the matter with the Criminal District Court judges.

An order issued Tuesday by U.S. District Judge Lance Africk, who is overseeing a consent decree mandating sweeping reforms at the city’s jail, said the sheriff, who has consistently avoided appearing in Africk’s courtroom during the extensive jail-related litigation, would be required to address changes his office has made “which may affect the administration of justice” at the local courts.

The order followed a day of disarray in which many inmates arrived late — or not at all — for scheduled court appearances. One defense attorney said an entire of group of defendants had their hearings postponed in Municipal Court because “almost no inmates” were transported to the court.

Simone Levine, executive director of Court Watch NOLA, said that, “in many cases, incarcerated pretrial defendants and witnesses were not produced at all” by the Sheriff’s Office on Tuesday.

“It’s a mess,” added Derwyn Bunton, the chief public defender for Orleans Parish.

Blake Arcuri, an attorney for Gusman, said the issues were only temporary and had been triggered by the opening of the new 1,438-bed facility and the simultaneous closing of several aging jail buildings, including Old Parish Prison. The problems were resolved before Wednesday’s court sessions, he said.

“Moving more than 1,100 inmates across a series of buildings is not an easy task,” Gusman said in a statement.

The closing of Old Parish Prison, a structure directly connected to the Criminal District Courthouse, has raised questions about whether inmates will continue to be ushered into court through a holding area of OPP known as “the docks.” Gusman has said he wants to decommission the docks, in part because of security concerns in a building that is no longer fully manned by deputies who could be called as backup in case of a disturbance.

A corrections expert monitoring the jail reforms referred to the docks this summer as “not an appropriate place for housing inmates while they’re waiting for court.”

Further complicating matters has been the sheriff’s indefinite relocation of some 250 pretrial inmates — many of whom face serious felony charges such as murder — to jails several hours away in East Carroll and Franklin parishes.

Gusman has said those inmates would not fit in the new jail. But several defense attorneys said they were blindsided by that move, which will greatly restrict their access to their clients.

“I think it’s a little early to tell how much of this (confusion over court appearances) is due to the shipment upstate and how much of it is due to the transfer to the new facility,” said Colin Reingold, special litigation director for the Orleans Public Defenders Office. “It didn’t sound like (the Sheriff’s Office) had a solidified system for knowing where the inmates were housed in the new facility so they can efficiently bring them to their court appearances.”

Another defense attorney, Kevin Boshea, said he learned over the weekend that Clifford Williams, a client of his scheduled to stand trial Tuesday in a second-degree murder case, had been among the inmates sent several hours away last week. He filed a last-minute motion to postpone Williams’ trial.

Sheriff’s Office officials said they had tried to select inmates for the move who were not scheduled for trial in the coming weeks.

“How do I prepare a man to testify in his own defense when he’s on trial for his life if I can’t get to him?” Boshea said. He proposed that any inmates who have cases set for trial within 30 days should be housed in Orleans Parish.

“If we don’t rethink our procedures, the system is going to come grinding to an absolute, screeching halt,” Boshea added. “It’s not rocket science.”

Follow Jim Mustian on Twitter, @JimMustian.