OVERLAND PARK, Kan. » The prosecution of a Planned Parenthood affiliate here, the first such criminal case in the nation, has been treated locally as something of a proxy in the battle over abortion rights. Derided by supporters of the organization as politically motivated, the prosecution was celebrated by opponents as the capstone of increasingly aggressive actions here and elsewhere against Planned Parenthood, which provides abortions and other services at health clinics around the country.

So it came as a surprise to many this month when county prosecutors here announced that after years of battling, they had been forced to drop nearly half the charges, including all of the felony counts, citing faulty record keeping. The misdemeanor charges, which involve accusations of failing to fully determine viability before performing some abortions, are still pending.

The revelations that documents in the case had been destroyed years ago added a fresh dose of controversy to what has been a particularly strange chapter in the abortion fight in Kansas, a messy and tangled case that emerged out of a wide-ranging investigation into abortion providers and that has been consumed by allegations of misconduct by political leaders on both sides of the issue.

The state’s vocal, and increasingly empowered, contingent of abortion opponents, including a number of Republican elected officials, wondered aloud whether a cover-up was to blame. And Planned Parenthood of Kansas and Mid-Missouri questioned whether prosecutors were encouraging conspiracy theories as a way to blame abortion rights supporters while abandoning a losing case.

As the sides swapped accusations, the state attorney general requested an investigation into the document destruction, which is now under way.

This year had already seen escalating conflict over abortion in Kansas, the staging ground for some of the most divisive battles in the nation over the issue. Gov. Sam Brownback, a Republican who strongly opposes abortion, approved a series of restrictions, most notably establishing new regulations on clinics that nearly forced two of the three abortion providers in the state to shut down before a federal judge blocked them. Another rule prohibiting Planned Parenthood from receiving federal family planning money was also blocked by a federal judge.

Peter B. Brownlie, president and chief executive of the local affiliate, praised the dismissal of the most serious charges and said the organization would prevail on the remaining ones.

"There’s no question that political opponents of Planned Parenthood and abortion would have been emboldened by a conviction, particularly on a felony charge," he said.

The case emerged from a long investigation by one of the state’s most polarizing elected officials, Phill Kline, who had used his position as Kansas attorney general and later as Johnson County district attorney to crusade against abortion providers, earning a series of official rebukes along the way for his tactics, including a recommendation last month by a state board that he be prohibited from practicing law in the state.

Although the investigation, started in 2003, initially centered on explosive allegations that abortion providers were not reporting all cases of child rape, the charges Kline eventually filed in 2007 were far less dramatic, including that Planned Parenthood failed to maintain copies of abortion paperwork (a misdemeanor) and, fearing detection, completed the paperwork after an investigation was begun (a felony).

At issue was the fact that the copies of the "termination of pregnancy" reports filed with the state had different handwriting than those kept at the clinic. Planned Parenthood said the reports were different because the copies were made by hand rather than on a copy machine.

As the case was being prepared for trial, Steve Howe, the Johnson County prosecutor who took up the case in 2009 after defeating Kline in a Republican primary, discovered that the records that were to be used as evidence had been destroyed years earlier, the originals by the Department of Health and Environment and the only authenticated set of copies by the attorney general’s office. As a result, Howe told a judge this month that there was no longer enough admissible evidence to proceed with 49 charges, including 23 felonies.

Mary Kay Culp, executive director of Kansans for Life, which opposes abortion, was among those who noted that the governor at the time, Kathleen Sebelius, now secretary of health and human services, was a strong supporter of abortion rights and that the attorney general then, Steve Six, was her appointee.

"It’s beyond belief that evidence was purposely destroyed, but I believe that’s what happened," Culp said.

But supporters of abortion rights disputed the allegations that the documents were intentionally, rather than routinely, destroyed, and questioned why they had not been requested and secured previously.

"It’s a red herring to avoid having to walk into court, present the case and lose on the merits because there was never any crime," said Pedro Irigonegaray, a lawyer for Planned Parenthood.

An official investigation is under way at the request of Derek Schmidt, the Republican attorney general who defeated Six in 2010. He wrote to the Shawnee County sheriff this month requesting an inquiry, because documents pertaining to abortion-related investigations and prosecutions had been destroyed by the attorney general’s office in 2009 after Dr. George Tiller, an abortion provider who was later murdered by an abortion opponent, was acquitted of criminal charges.

"Sufficient questions exist to require a full and complete investigation of this matter to determine what actually happened," Schmidt wrote.

A spokeswoman for health and human services said Sebelius "had no knowledge of the document shredding issues."

Six, who had a nomination to the federal bench blocked because of opposition from abortion opponents, did not return a call for comment.

Kline, the former prosecutor who now teaches at Liberty University School of Law in Virginia, said he believed the destruction revealed pervasive corruption in state government.

"How does it end?" he asked. "I don’t know, but I don’t expect the judicial system to get to the truth."

© 2011 The New York Times Company