I think you’re probably right, NARA itself might not have a comprehensive list of these documents.

But, as someone who once upon a time worked with classified materials in the military, our department had a register of every document, when & who checked it out and when they checked it back in. When documents needed to be destroyed two people did the job and both had to sign the register.

Somewhere, someone had a local register and had to realize these documents went missing. But, they must not have been officially checked out, otherwise they would have known where to retrieve them.

All very strange. Kind of reminds me of the Pumpkin Papers.