The archivists probably have a really keen idea of what is and what isn't missing, based upon things that they've gotten out of other offices, like the vice president's office and things that were deposited from the secretary of state, for example. There are a lot of papers that are referenced and cross-referenced, multiple copies or multiple things going in and out of offices.
One scholar did a study of the presidents' annual Christmas speech at the Ellipse in Washington. He looked at how the speeches — from the Roosevelt administration to the present — developed, and it was kind of a ring-around-the-rosy inside the West Wing and within the departments. What went in, what went out, what went in, what went out; who won and who didn't win. Everybody left their marks on the speeches. All those changes and requests appear in documents, and if part of the conversation is missing from the National Archives, it's obvious.
We know from other presidents' records that really comprehensive records are kept via daily manifests of what the presidents are doing. And while I am not a historian, it's not unreasonable to assume that the other departments and agencies likewise have daily manifests of their top officials. So if they know that someone at an agency sent something over to the White House that was this or that, and it came back from the White House with this or that, then there should be a document somewhere that's got something from the White House on it — and if you're missing that, that's a problem.