The hijacker registered for the flight under the name “Dan Cooper.” A reporter’s mistake resulted in him becoming known as D.B. Cooper. A real Dan Cooper was investigated and cleared.
The bills were not marked. They were photographed. The serial numbers were circulated and eventually published. But cross-checking $20 bills against a comprehensive list would have been remarkably tedious and essentially pointless... there was no reward for finding any of the bills and a found bill wouldn’t have yielded much information in the end...