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TRACY — There’s a battle over charter schools and how they operate. Acacia Elementary and Middle schools are now in the thick of a legal battle for the hundreds of students they educate.

It’s the ABC’s of learning but in a modern way at Acacia Middle School.

The classrooms nearly shuttered their doors in July.

The New Jerusalem School District in Tracy oversees Acacia Middle and Elementary Charter schools, both in Stockton.

They are public schools that are independently run but government funded. In July, the district attempted to revoke the schools’ charter. The issue is how the company that operates them, Tri Valley Learning Corporation ,or TVLC, is running their finances.

“Due to their financial mismanagement and mixed test scores we revoked their charters,” said David Thoming, the superintendent of New Jerusalem School District.

A judge granted a temporary restraining order against the school district allowing TVLC to continue operating the schools.

Superintendent Thoming claims problems still exist.

“They’re still not being truthful with us,” he said.

The school district said TVLC has a negative budget of a million dollars and that it has not provided an updated budget for Acacia. Other concerns include enrollment.

“We have yet to hear correct enrollment numbers,” Thoming said.

The interim CEO of TVLC, which operates Acacia and two other schools in Livermore, denies the allegations.

“We’re very honest every time they ask. They get our reports once a month,” said Dr. Lynn Lysko, the interim CEO of TVLC.

Lysko admitted there have been problems in the past. The company overhauled its leadership and since she took over in April, she said all the schools are run differently.

“I’ve been trying to clean up those mistakes,” Lysko said.

Another issue, accusations that TVLC funneled money from its schools in Stockton to those in Livermore.

“The students that need the most revenue in order for them to be successful are losing that because of something they want in Livermore,” Thoming said.

“That may have been, you know, past practice, but that’s not how I am operating,” Lysko explained.

Both sides said they are protecting their students’ best interests.

“It’s a very sad situation because at the end of the day, it is the students that get hurt,” Thoming told FOX40.

“We want to run excellent programs and give parents a choice,” Lysko said.

Both sides are expected in court later in September.

The New Jerusalem School District told FOX40 it’s ready to walk away, and TVLC is already searching for another district to take over.

TVLC is hoping Stockton Unified will take the job. We reached out to that district they said the Acacia schools petition are under review.