Five months ago, when Illinois schools Superintendent Carmen Ayala learned students were being repeatedly shut inside small rooms alone as punishment and physically held down on the floor, she said she cried. She vowed it would never happen again.

But Illinois State Board of Education officials negotiated with a key legislative rule-making committee to allow schools to use prone restraint for one more school year, aiming to phase out its use by July 2021. The decision last week came after a few small schools — including one whose advisory board includes state lawmakers — mounted letter-writing campaigns and direct appeals to government leaders.

State education board members already had relaxed the emergency ban that prevented children from being secluded by themselves, though with clearer direction on when isolated timeouts can and can’t be used and, for the first time, state oversight. The board, however, had remained firm on not allowing face-down, or prone, floor restraints because they are too dangerous.

“It is surprising that all of a sudden another group that has the final say would put all of that feedback from citizens and good research and good data to suggest that is not safe or healthy for children aside,” said Kevin Rubenstein, president of the Illinois Alliance of Administrators of Special Education.

The initial changes, including a declaration by Gov. J.B. Pritzker that “isolated seclusion will end now,” came in response to a Chicago Tribune-ProPublica Illinois investigation, “The Quiet Rooms,” that documented the misuse and overuse of seclusion and restraint in Illinois schools.

Those emergency measures were set to expire this month. Permanent rules must be approved by the Joint Committee on Administrative Rules, which reviews new and existing rules proposed by state agencies. The bipartisan committee is made up of 12 legislators, including some of the state’s most powerful politicians.

The committee met Tuesday in Springfield amid the coronavirus pandemic in a room closed to the public. Audio was streamed on the committee’s website; the meeting lasted 12 minutes and there was no discussion.

Legislation pending in the House and Senate, which would supersede ISBE’s rules, still could ban prone restraint and isolated seclusion, and state education officials said they would review the use of prone restraint during the next year. They hope to eliminate it after that.

ISBE spokeswoman Jackie Matthews confirmed that the decision to allow prone restraint came after some schools, most of them private, said they were concerned they didn’t have enough time to transition to other methods. She said the restraint should be used rarely and with the idea that it will be phased out.

“ISBE absolutely will revisit the use of prone restraint either through legislation or future rulemaking before the one year-extension expires,” she wrote in an email.

The ProPublica Illinois-Tribune investigation documented more than 35,000 seclusion and restraint incidents involving students in 100 school districts over a 15-month period beginning in the fall of 2017. Although state law then allowed seclusion and restraint when students were in danger of harming themselves or others, reporters found that in one out of every three incidents of seclusion, school workers hadn’t cited a safety reason; for incidents of physical restraint, the ratio was one in four.

About 24 hours after the investigation was published, ISBE imposed an emergency ban on secluding students alone and on floor restraints, and pledged to make it permanent. Advocates for students with disabilities saw the bans as a victory; real change seemed imminent.

The new rules still provide more protections for students than the state law that had governed the practices for 20 years. Seclusion rooms can no longer have locks, and employees can’t hold the doors shut to keep children inside. Rules now specify that timeout and restraint can be used only when there’s an “imminent danger” of serious physical harm. Schools now are required to report every incident to the state and provide more employee training.

But at least three suburban Chicago schools — two private, one public — mobilized to lobby state officials, flooding them with comments supporting isolated timeout and prone restraint.

Through a Freedom of Information Act request, the Tribune and ProPublica Illinois obtained more than 325 public comments filed with ISBE in response to its proposed rules.

At least 101 of the 149 letters that advocated keeping prone restraint — nearly 70% — came from two private schools, Giant Steps and Marklund Day School, and the A.E.R.O Special Education Cooperative, a public school.

“As a staff member at Marklund Day School, I have personally performed a safe prone restraint more times than I can count,” began each of the 350-word letters that about 30 employees of Marklund, a suburban school for students with autism, filed with the state.

The nearly word-for-word letters — sent by teachers, aides and other workers — urged ISBE to allow prone and supine, or face-up, restraints at school and touted the improvements shown by Marklund students with “maladaptive” and aggressive behavior because employees were allowed to physically restrain them. State enrollment data shows that Marklund Day School serves about 70 students.

Marklund workers worried that ending prone restraint immediately would harm students who “needed that momentary brief, required relaxation to help them calm and regain their composure,” Marklund’s director of education, Paula Bodzioch, said in an interview. Workers weren’t trained to use other restraint systems.

More than 60 letters — the most from any school — were written on behalf of Giant Steps, a 160-student school in suburban Lisle for students with autism.

Parents, employees, siblings — even friends of parents — sent identical letters, sometimes without personalizing the suggested language: “I am a (parent, staff member, friend of/escribe su nombre aqui) Giant Steps Therapeutic Day School in Lisle, IL and I am contacting you to submit the following comment(s) on the proposed final rules.”

The letters urged ISBE to remove the ban on face-down restraints, which both Giant Steps and Marklund say can be safe. More than 30 states have banned prone restraint in schools because the risk of asphyxiation is believed to be greater when adults put weight on students in that position.

Among those who advanced Giant Steps’ argument was the chief of staff for one of the Illinois House’s most powerful members, Republican leader Jim Durkin. The school’s suggestions were emailed to ISBE and the legislative rule-making committee by House staff, records show.

Durkin and five former Illinois lawmakers sit on Giant Steps’ eight-member advisory board, along with two lawyers. The school’s director, Sylvia Smith, said in a recent interview that she regularly speaks to Durkin and other legislators and has made building relationships with them a priority.

“When you know them and have their cellphone numbers, they will take your call,” Smith told reporters during a tour of the school in February.

Smith held an open house for lawmakers in January to make her case for seclusion and restraint, she said, and a dozen attended. The school, the first licensed therapeutic day school in Illinois for students with autism, aims to help children until they can transition to public schools.

“When [seclusion and restraint] came up, leader Durkin called and said, ‘What do you think?’” Smith said. “I told them we need help.”

Durkin did not respond to requests for comment.

Prone restraint is one strategy the school uses to help students “maintain stable behavior and return to the classroom,” Smith said last week.

Rep. Keith Wheeler, a North Aurora Republican and co-chairman of the Joint Committee on Administrative Rules, also listened to Giant Steps and Marklund. Both schools are in his district.

Wheeler said he visited Marklund recently and saw employees use prone restraint on a student. They explained why they preferred it. Wheeler described learning about challenging students who bit or gagged themselves and who bite staff members, even through Kevlar gloves.

“They made it very clear to me that not only are we trying to protect the student from harming themselves or other students, but also to protect them from harming the staff,” Wheeler said. “I want to pause before we eliminate this option. How can we limit this enough to just these specific students who may benefit from it until we find an alternative that’s better for them?”

At least 13 comments came from workers at A.E.R.O, a public special education cooperative in suburban Burbank, which lobbied ISBE more than any other public school to keep prone restraint. A.E.R.O. is one of the few public schools that used the restraint regularly, according to “The Quiet Rooms,” which found that about two dozen districts used floor restraints nearly 1,800 times in the 15-month period analyzed.

A.E.R.O. executive director James Gunnell declined to comment.

ISBE’s change of course last week surprised educators who, just weeks ago, heard the board vote to eliminate prone restraint. In response to public comments from Giant Steps, Marklund and others asking to keep prone restraint legal, ISBE wrote: “It’s best practice to prohibit prone physical restraint.” That echoed Ayala’s earlier comments to reporters: “Under my watch, I cannot — I will not — allow it to continue.”

While prone restraint will be allowed next school year, ISBE told school officials in an email they should “actively pursue” alternatives and training.

In a December interview, Heather Calomese, ISBE’s executive director of programs, said prone restraint was too dangerous to use. Staff could be injured, she said, and the safety risk to students is too high. Staff members “could potentially block an airway. They could put pressure on a part of a body that would restrict airflow,” she said.

The rules include a “sunset” provision that means the permission to use prone restraint in schools will expire on July 1, 2021. ISBE will have to go through the rule-making process again unless legislators ban it in the meantime, Matthews said.

Until then, schools can use both prone and supine restraints in narrow circumstances and only when “less restrictive” interventions have not succeeded. A trained adult must observe the restraint, and extra review will be required if a student is restrained on the floor twice within 30 days. The restraints must end as soon as the threat of serious physical harm ends.

Wheeler, who co-chairs JCAR, also said he hopes to collect data about the use of prone restraint over the next year.

Chris Yun, who oversees education policy for AccessLiving, a Chicago disability-rights group, questioned what data needs to be collected to understand whether prone restraint is too dangerous to use in schools.

“They want to see if somebody dies? That’s the data?” Yun asked. “I’m really speechless.”

State Rep. Jonathan Carroll, a Northbrook Democrat, said he is working on amendments to a proposal he made in November that would address seclusion and prone restraint. He said he is sympathetic to schools that would have to find other ways to manage challenging student behavior. But Carroll, who was secluded as a child, said he also is focused on the harm that seclusion causes.

“We recognize that there’s a lot of work to be done in this area and we’re willing to work with everyone on solutions,” said Carroll, a former special education teacher. He said it was “upsetting” that schools lobbied for their position through the rule-making process and that he is “disappointed in JCAR.”

Amber Patz said her hope for change has diminished. Her son, Dalton, 11, was repeatedly restrained and put in seclusion at The Center, an elementary school in East Moline for children with disabilities.

“We are coming up on almost six months into this and already (Pritzker) is backpedaling or allowing those around him to backpedal,” Patz said. “He made a promise to the children.”