When Hank Reardon and Dagny Taggart searched the abandoned 20th Century Motor Company, they found the prototype of John Galt's motor along with some documents describing it. However, the documents related to it were incomplete, missing what Robert Standler and some other characters described as the most important parts (e.g. John Galt's definition of energy and some other basic facts).
John Galt later told Dagny that he left the prototype there because it was their rightful property, given that they had paid him to develop it. He also wasn't too concerned that they'd actually use it.
What about the manual? It seems odd that a lot of the manual was there, but it was only missing the most important parts. For example, if someone used the missing pages as fuel for a fire or something like that (like a lot of the other paper in the plant was), wouldn't they have just burned the whole thing? Why bother using only a few pages? Did John Galt (or William Hastings, John Galt's boss who later joined the Strike) remove the most important pieces? If so, why didn't they regard the manual as the new owners' property, too? If they didn't remove it, why did John Galt and William Hastings risk someone reading the documents and learning the secret of the motor?