One possible alternative explanation could be that the documents in the archives from the Clinton era (1) were not properly classified and accounted for when created due to the Clinton attitude towards security, (2) are so voluminous, and (3) are now not being used regularly in the way we ordinary think of a top secret-SCI document being distributed [with "Copy X of Y Copies" and "Page a of b Pages" on every page and someone having signed for each and every page every time the document leaves a vault file] that the documents have not yet been fully and completely inventoried and logged into the normal classified records system.
That would account for the fact that what we'd think of as normal procedure:
i.e. What I'd have expected:
Guard: "here is a list of the documents, Mr. Berger. Please tell us what you want to see."
Berger"OK, guard x, please bring me #2, #56, and ### etc" "OK, Mr. Berger, here they are. Please sign the log here for each document, inspect to see that all pages are present and initial the log for the presence of each page right along with me"
and when he was ready to leave:
Guard: "You're ready to leave now Mr. Berger? Hope you found what you needed. Let's just get you signed out now. Let's see, my list shows you have the follwing documents (recite list). Let's get each one logged in and quickly check each page to make sure they're all there. I know it's a pain, sir, but it is the procedure."
Unlikely, but possible.
I had considered that. At the very minimum, there is a security manual (itself classified) for that facility that was approved by some overseeing agency - I wonder if the Archives are vested with that authority on their own. While it's quite possible the approved security manual is in need or review and revision, I've no doubt that - at minimum - if the existing proceedures had been followed, this wouldn't have happened.