Another criminal backdating investigation is officially over.

Two weeks ago, prosecutors in the Northern District of California U.S. Attorney’s Office told defense lawyers that their stock option probe of KLA-Tencor and its former CEO would conclude, and that no indictments would be filed.

“They told us they were closing the file, that they were not pursuing it,” said Kenneth Schroeder’s attorney, Elliot Peters of Keker & Van Nest. “We had had a lot of dialogue with them about it. They made a very reasoned and fair decision, in my mind.”

The Justice Department had been eyeing KLA since the company was one of the first named in The Wall Street Journal‘s 2006 expose of stock option backdating. KLA eventually restated $370 million in earnings.

A government spokesman declined to comment on KLA.

Another executive under prosecutors’ backdating microscope, Apple’s former general counsel, Nancy Heinen, also was told earlier this year that she would not face criminal charges. She recently settled her SEC case for a $2.2 million fine.

Schroeder, though, is battling the SEC in the Northern District. Securities regulators accuse the former chief executive of ignoring advice from the company’s counsel and backdating options. Schroeder backdated many of his own options, the SEC alleged. The executive denies these charges.

Currently Schroeder’s civil defense lawyers at DLA Piper have been battling to depose company witnesses and to view lawyer notes taken in the course of an internal investigation conducted by Skadden, Arps, Slate, Meagher & Flom. KLA contends that Schroeder is free to depose witnesses as long as he agrees to confidentiality terms.

DLA’s Shirli Weiss calls those conditions “unacceptable.”

“KLA seeks to avoid a ruling on what has clearly been a pervasive waiver of the attorney-client privilege,” Weiss wrote in court papers.

A hearing on these issues is scheduled for Sept. 23 before U.S. Magistrate Judge Howard Lloyd in San Jose.

The SEC has also sued former KLA general counsel Lisa Berry, claiming she backdated options there and then exported the practice when she became in-house counsel at Juniper. Berry argues that outside lawyers at Wilson Sonsini Goodrich & Rosati didn’t raise any red flags about KLA’s stock option practices, and thus she didn’t know she did anything wrong.

Last week, U.S. District Judge Ronald Whyte struck some of the SEC’s claims against Berry for the second time, including its attempt at disgorgement. Whyte gave the government one more chance to amend its complaint.