The problem rises from assuming that these ever [i]were[/i] canon. In the eyes of George Lucas, the closest a game ever came to being canon was The Force Unleashed. None of the books ever were canon to him, nor were the games. And that's how it still is. But that doesn't mean we can't keep enjoying what we have. Until outright contradicted, these characters and stories can exist as they always have. For now, I doubt they're going to go all the way back to the time of KotOR to throw that one out. And many other Star Wars games feature new characters in new situations that occur far from the action anyway (a la Kyle Katarn defeating Imperial warlords and such). Are they overwritten? Not really. They can still exist as they are, until they've been replaced. Besides, canon's a fickle bitch right now, and they'll surely make callbacks to EU sources already in existence going forward (apparently they're already doing that with Rebels). By incorporating old things in new films, they'll solidify themselves in canon. But the parts that aren't replaced can still exist just fine, for now. The Clone Wars made a mention of Darth Bane. Darth Bane (if I'm remembering correctly) picked up some of what he'd learned from Revan. Bane, with mention in the Clone Wars, is officially canon. Now whether they'll change his past or leave it be has yet to be seen.