Nearly $200,000 that’s been frozen in an escrow account in the name of Warren County Circuit Clerk Shelly Ashley-Palmertree will be transferred to an account to be set up by county officials, and most of the money is expected to be returned to county coffers, the Office of the Mississippi State Auditor says.

An additional $340,000 or more remains in dispute in the state auditor’s review of fee accounting practices in the circuit clerk’s office that has been unresolved since 2006.

The $199,588 that Auditor Stacey Pickering said Thursday afternoon would be repaid represents amounts Ashley-Palmertree and her father, Larry Ashley, whom she succeeded in office in 2004, withdrew from criminal and civil court statutory fee accounts in excess of what state law allowed, said Lisa Shoemaker, director of communications for Pickering.

“The majority of the money will go back to Warren County,” Shoemaker said today. “When we got to a point where we had a final number, and got a final payment from (Ashley-Palmertree), we felt confident releasing those figures. As far as we are concerned, the money has been there this entire time, and just some minor bookkeeping is needed to determine how much goes into the Warren County general fund and how much is remitted to the state.”

Ashley-Palmertree, who is seeking re-election to the circuit clerk’s spot in voting Nov. 8, confirmed that the escrowed account is to be transferred to the county but said the money is not intended for the county to spend yet.

County Administrator John Smith, who generally handles the county’s finances under the oversight of the Board of Supervisors, said this morning that he had not been notified of the decision and said Chancery Clerk Dot McGee most likely would be notified by the state. McGee was out of the office this morning and unavailable for comment, and an employee in that office said she was not aware of an account being set up.

Ashley-Palmertree said Pickering’s office instructed her in a letter about two weeks ago to hire an independent certified public accounting firm, essentially to get a second opinion on the disputed transactions in those criminal and civil court accounts.

“That firm is also supposed to address all the issues that (the county’s auditing firm) raised,” she said. “They will be working with the state auditor’s office to bring everything into compliance to the state auditor’s satisfaction.”

Pickering’s office said in February that fee practices in the circuit clerk’s office were under investigation. Ashley-Palmertree, however, has said the term is inaccurate and the effort has been a cooperative one.

“I’m glad we finally have gotten to this point,” she said today. “This is the guidance I have been looking for.”

Thursday’s announcement represents only a part of what’s been in dispute for years between Ashley-Palmertree and Bridgers & Company, the local certified public accounting firm hired to conduct Warren County’s annual audits.

“Other findings have been cited in the auditor’s reports that are part of a completely separate investigation that is still ongoing,” Shoemaker said.

According to the 2010 Warren County audit report, those findings include about $293,000 Ashley-Palmertree collected between 2006 and 2010 in excess of her state-mandated salary cap of $90,000, plus $49,000 in unsubstantiated sub-contractor fees from 2010.

It’s not clear if subcontractor fees remain unresolved from prior years, and Shoemaker would not say how much money is still at issue or offer a guess as to when Pickering’s office will complete its inquiry.

“I can’t comment on anything related to what’s still under investigation,” she said. “These financial matters are sometimes very complicated, and they take time. We’re pleased to have this part finished at least.”

The amounts Pickering says have been resolved — $164,858.60 from Ashley-Palmertree and $34,729.56 from Ashley — were identified through examination of court accounts from 1999 through 2010, he said.

The county’s 2010 audit report notes that $137,995 had been in the escrowed account for five years, and Shoemaker said additional amounts had been paid into it, the last a $5,059.88 payment by Ashley-Palmertree on Sept. 6.

Ashley-Palmertree is seeking her third term as circuit clerk. She won the Democratic Party’s nomination in August and faces Republican David Sharp, a school teacher, and independents Jan Hyland Daigre, an insurance executive and fomer member of the Vicksburg Warren School District Board of Trustees, and Robert Terry, a real estate broker associate, on Nov. 8.

Her father held the circuit clerk’s job for four terms, 16 years, before she was elected.