In DS9's "Inquisition", Sloan explains that Section 31 has been around since the inception of the Federation, and that they were officially part of the original Federation Charter. Because Enterprise takes place before the foundation of the Federation, Section 31 should not exist yet. However, it is implied in this episode (and the last one) that they have already been in operation for years by this point. Harris also tells Archer what part of the Starfleet Charter allows them to operate.

Millions of Klingons are transformed into the type of Klingons we see in The Original Series, and it's stated that this condition will be passed onto their children, but some day, it may be reversible.