It wasn't 40 years ago that the National Archive suddenly mysteriously found in the Library of Congress the bills for expenses of Gen George Roger Clark's Illinois expedition during the Revolutionary War. Congress told General Clark when he asked for payment for his expenses that they had never recieved those bills and refused to pay for the Expedition. Read the footnotes in a couple of Allen Eckert's or Alexander Thom's books. They are a couple of the best historical researchers I have read after Civil War or otherwise.
The fact of the matter is that the Combined Muster Rolls are not the original records and are not complete. They are just the best records that we presently have and most likely will have.