A few months ago, parents, teachers, community partners and staff from Boston Public Schools gathered at Blackstone Elementary School in the South End.

“The district came in, and they put up flip chart papers on the wall and they said different things like ‘English language learners’ or ‘inclusion classrooms' or ‘family supports' or ‘partnerships,’" said Ariel Branz, senior parent organizer at St. Stephen’s Youth Programs, which runs the Blackstone’s library and a parent mentor program. "Then families and teachers were asked to put up stickers for each one, saying which they valued more.”

Branz said when people at the meeting refused to participate, the district said it was only a thought exercise to understand their priorities.

"And then, the next meeting, they came back with a budget that was still missing a lot of support for inclusion and partnerships, and then they said, ‘Well, this is because this is the priorities that you chose and you told us at the last meeting," said Branz.

The Blackstone is facing what staff say is a budget shortfall of more than $400,000 under the district budget that the Boston School Committee approved March 27.

The school will have to eliminate two staff positions that work with special needs kids and two that do community engagement. They'll also cut back several community partnerships.

What the Blackstone is going through financially reflects a statewide pattern. When schools in Massachusetts struggle to succeed, they have the option to take on special statuses designed to give them more autonomy and flexibility to improve performance. But when schools transition back to regular status, they experience de facto budget cuts that undermine whatever progress those schools have made.

In 2010, the Blackstone was one of the lowest-performing schools in the state. Thirty percent of third-graders failed the state's MCAS test for reading. The school entered turnaround status, a designation that adds more staff support and more class time for students.

Three years later, the school had improved. But Bill Wolff, president of the fund-raising group Friends of Blackstone School, said the transition was bittersweet.

“When it came out of turnaround status, the good news is that we improved the school performance," he said. "The bad news is that we lost about $800,000 in funding.”

Blackstone had been receiving extra money through the state from a federal grant. The school received $2.25 million over the course of three years. But once it moved up to innovation status, most of that money disappeared.

Now, five years later, the school is moving from innovation status back to the status for regular or traditional schools, so it’s experiencing another budget shortfall.

“If you look at how the money is allocated, it defies some logic," Wolff said. "Just because our status changed from innovation to regular school doesn’t change the needs of our kids. For us to have a system where when one changes status, the funds get changed dramatically — it doesn’t make sense.”

Wolff also said the current model discriminates against already-marginalized schools.

"Those schools that have the biggest issues happen to be black and brown, and those schools happen to have very low political influence," he said. "The system's rigged against those folks, because in order to give them the money that many of us think they need, it's got to come from someplace. And the schools that are getting the money aren't really very interested in giving it up."

A spokesman from Boston Public Schools said the district “explicitly communicated the budgetary ramifications” of leaving innovation status to staff at the Blackstone, and even granted an extension to ease the transition.

Because of its latest status change, the Blackstone winds up with less money because it has to pay more in teacher salaries.

“It’s becoming a traditional school in the same way that it was 10 years ago," said Alex Sullivan, a third-grade teacher at the Blackstone. "The budget formula once again will change, and pretty much the only area of the budget that’s affected is the way that positions are funded.”

She said each school in Boston pays the district for teaching services by paying a certain amount per teacher. Most Boston Public Schools pay the average teacher salary, about $99,000. But under innovation status, schools have the option to pay actual salaries.

“Because we have a lot of new teachers, the salaries were lower [than the average salaries]," Sullivan said. "So the money that was left over in the budget stayed with our school.”

Now that the Blackstone is back to traditional status, it’s paying more per teacher, so the school is left with less money to spend on support staff, like the positions they'll cut next year.

"There are ways that we should be legally and appropriately servicing our students with special needs and with behavioral needs that just aren't happening because the human power isn't there to do it," Sullivan said.

Maria Burke's position as a school counselor was on the chopping block until the Blackstone took money from community partnerships and the district allocated additional funds.

"When I heard that they were going to eliminate social-emotional support for the school, I was very afraid. I was shocked, and I was angry," Burke said. "I was angry because I felt that my students weren't going to get the support that they needed."

Burke said she feels that staff voices were heard since the district added $95,000 to the Blackstone's budget after the initial proposal. But she said Boston's process of allocating money to schools still doesn't make sense to her.

"I am unclear, personally, about where that money is all of a sudden coming from, if at first it was gone... [and] there was no getting it back," she said.

The state classifies nearly 90 percent of Blackstone students as “high need,” meaning they have disabilities, are or once were learning English or come from low-income households.

“We’re stressed out, not just because — we need incomes and we have families to support — but because we care so deeply about our students," Burke said. "And to know that our students are going to be deprived of the things that they need weighs really heavy on us.”

Burke said she’s checking in on children all day, from the first bell until dismissal. During an interview with WGBH News, she got a visit from 10-year-old Joselis.

“It’s nice to have somebody, like, in this building, to help me when I’m stressed," Joselis said. "There’s, like, some stuff happening that I don’t want to share with nobody else but Miss Burke.”

Burke is working with Joselis on a video project about women's equality, prompted by some boys teasing girls at school.

"These kids just want to be known," Burke said. "They want to be understood, and as young as they are, there's still many layers to them and a lot of these kids are mature way past their age because of the experiences they've had."

The city council and the mayor must sign off on the budget in the coming months for it to take effect.