Just glanced through the DOJ Brief, and there were a couple of interesting things I did not know:
When the 15 boxes were returned earlier in the year, NARA found classified documents that had been "unfoldered" (i.e. taken out of their folders containing the classified markings) and were intermingled with other records. It is an accepted rule of nature that documents are inanimate and do not remove themselves from folders and envelopes.
Some of the papers had been "torn up."
The DOJ had "multiple sources" of information that classified records remained at MAL after the attorney's certification to the contrary.
Per Chuck Rosenberg (former federal prosecutor) on MSNBC last night, not only are classified documents maintained in the brightly-colored large-font-labeled folders, but the documents themselves have individual classification markings for each paragraph. Once they are removed from the marked folders, anyone looking at the documents has immediate knowledge of their classification status.