Fortunately, Hawkeye, Wolverine, and Cloak remember what things were like before the change, and set out to change things back.
She usually does this in minor ways, but House of M was a different story.
As we’ve recently discussed on the site, Scarlet Witch’s gifts in the comics are slightly different than they are in the movies, as the hero on the page actually has the ability to change reality.
She suffers a serious breakdown after losing her two children (kind of a long story), and when the Avengers and the X-Men question whether or not she needs to be killed because of her unstable powers, she winds up creating a completely different and idyllic reality — one where mutants are the dominant species, and humans the minority.