"Our search of government records was complicated by the fact that some records we wanted to review were missing and there was not always an explanation. Further, the records management regulations for the retention and disposition of records were unclear or changing during the period we reviewed."
(GAO Report)

So, the retention and disposition of records were unclear or changing during the period we reviewed.

"The Center's Chief Archivist stated that from his personal experience, many of the Air Force organizational records covering this time period were destroyed without entering a citation for the governing disposition authority. Our review of records control forms showing the destruction of other records-including outgoing RAAF messages for 1950 -- supports the Chief Archivist's viewpoint."
(GAO Report)

So, the regulations were unclear or changing at this time, according to the GAO and the actions regarding a small portion of the records were not unusual! The GAO didn't even mention the destruction of the documents in their first draft report because they didn't think that the documents were important since all of the incoming documents at the 8th AF HQ and AF HQ were .

However, on June 14, 1995, Congressman Schiff and two of his staffers met with the GAO to discuss the draft report. Schiff was unhappy that they didn't discuss the destroyed documents and asked them to go back and re-look at it. Guess what? The GAO, who get their money from congress, suddenly decided that the matter was sufficiently important to put into the second draft of the report, and they stated it strongly that the documents were permanent documents and shouldn't have been destroyed.

The GAO made a mistake.  It sent a draft to Mr. W. G. Seibert, the chief of the Appraisal and Dispositions section at the NPRC and archivist there and knowledgeable on this subject. Seibert told the GAO that they were totally incorrect!

"A draft of this report was provided to DoD for comment....The Chief Archivist, National Personnel Records Center offered several comments clarifying matters dealing with records management. These comments have been incorporated into the final report where appropriate." And, what did Mr. Seibert inform the GAO in writing?

That regulations in existence at the time the records were apparently destroyed clearly state that records "accumulated at or below wing level  will be scheduled as one item and destroyed after two years.... It is clear from the forgoing that record management officials, if acting in accordance with agency regulations then in force, should have destroyed the records in question rather than transfer them to St. Louis."
(Seibert's emphasis in letter to the GAO)

So the documents should have been destroyed, and the only fault that anyone can find with the AF is that they didn't destroy all the documents as they were supposed to have done according to the regulations!

Seibert's statements unfortunately didn't get put into the GAO report! And Schiff didn't use the final GAO document to write his press release but used the totally incorrect 2nd draft of the report:

"It is my understanding that these outgoing messages were permanent records, which should never have been destroyed." It seems probable that the GAO didn't put Seibert's comments into the document to avoid making the congressman look bad.

What about the GAO's statement frequently quoted by UFO popular authors that: "We could not locate any documentation indicating that records of the 1395th Military Police Company (Aviation) were ever retired to The National Personnel Records Center or its predecessor depositories."

Boy, that really sounds bad!

Until you realize that the quote is taken totally out of context!  What isn't shown by the conspiracy buffs is: "Document disposition forms obtained from the National Personnel Records Center in St. Louis, Missouri, indicate that in 1953, the Walker Air Force Base (formerly RAAF) records officer transferred to the Army's Kansas City records depository the HISTORIES of units stationed at Walker Air Force Base. These HISTORIES included the 509th Bomb Group and RAAF for February 1947 through October 1947; the 1st Air Transport Unit for July 1946 through June 1947; and the 427th Army Air Force Base Unit for January 1946 to February 1947. We could not locate any documentation indicating that records of the 1395th Military Police Company (Aviation) were ever retired to The National Personnel Records Center or its predecessor depositories.

The July 1947 HISTORY for the 509th Bomb Group and RAAF stated that the RAAF public information office "was kept quite busy ... answering inquiries on the `flying disc,' which was reported to be in [the] possession of the 509th Bomb Group. The object turned out to be a radar tracking balloon." By his signature, The RAAF's commanding officer certified that the report represented a complete and accurate account of RAAF activities in July 1947. (Excerpts from the report are contained in app. I.) In addition to unit HISTORY reports, ..." (Emphasis added)

So, the GAO is clearly referring to unit histories in this section!

And, these units were way below wing level!