User blog comment:Leolab/Retroactive Unfair Battle Enforcement/@comment-5422903-20121124222758/@comment-143604-20121125194740

The original Duke and the Duke originating from Duke 3D are still the same person and are in the same continuity, even if no one else remembers the times he wore pink and watched Oprah anymore. There are still occasional references and call backs to his history in those first two games in the later stuff (most notably, a direct sequel to them in the form of a DLC campaign for Forever), so I think it's safe to say that his CIA training is still canon, albiet an obscure part of his history.