The SEC’s longtime policy of purging certain case files could make it harder for anyone to second-guess regulators’ decisions to drop inquiries without taking enforcement action.

That’s one of the implications of an August 2010 letter by a Securities and Exchange Commission official responding to concerns from the National Archives.

The official assured the National Archives that, as it reassessed its policy last summer, the agency responsible for policing Wall Street directed its staff to preserve documents.

“The documents subject to this hold include any correspondence, interagency memoranda or other documents supporting a decision not to open a formal investigation,” wrote Samuel J. Waldon, assistant chief counsel in the SEC’s enforcement division.

For more than a decade, the SEC had instructed its enforcement staff to dispose of documents obtained as part of inquiries that did not lead to full-fledged investigations.

An SEC employee named Darcy Flynn alerted the National Archives and Records Administration to the policy last year, and the federal record-keeping agency asked the SEC for an explanation.

The history was publicized last week, when Sen. Charles E. Grassley (R-Iowa) released a letter from Flynn’s lawyer alleging that the agency illegally destroyed records.

Grassley argued that the destruction of records could cause other harm: It could make it harder for the SEC to detect patterns over time, and it could deprive the agency of information that could be useful in future investigations.

The SEC has been on the defensive about its decisions not to pursue certain investigative leads, most notably tips about Bernard Madoff, who for years got away with a massive fraud.

Flynn’s lawyer, former SEC official Gary J. Aguirre, suggested that decisions to drop cases were influenced by the revolving door that ties the SEC to the industry it polices.

The files that the SEC for many years instructed employees to purge were known as MUIs, or “matters under inquiry.”

Whether the SEC violated federal law is an open question.

SEC spokesman John Nester declined to say, citing an ongoing review.

Aguirre has argued that the SEC was required to retain records typically found in MUIs for at least 25 years.

The answer may be riding on the definition of MUI — more specifically, whether that is just another term for “preliminary investigation.”

A “Records Retention Schedule” from 1997, spelling out which records the SEC was supposed to preserve and for how long, says that investigative case files, “including case files relating to preliminary investigations,” should be destroyed 25 years after the case is closed or, if they were especially important, kept permanently.

The SEC spokesman said an SEC enforcement manual “clearly distinguishes between matters under inquiry and investigations.”

But the SEC’s August 2010 response to the National Archives made no such distinction.

“The MUI system was originally created as an electronic database for tracking preliminary investigations,” the SEC’s Waldon wrote.

“Over time, enforcement staff began to use the term MUI to refer to a preliminary investigation, or the period of investigation prior to a formal investigation,” he added.

The National Archives and Records Administration has sent mixed messages. In a statement last week, it said MUIs were not covered by “a NARA-approved disposition schedule.” But it said that meant the SEC did not have authority to dispose of the records.

If the SEC treated MUIs and preliminary investigations differently, there should be ample proof for ongoing probes to uncover — the preserved files of countless preliminary investigations.