Not an author, but I suspect that a similar "issue" cropped up when the original TOS movies and TNG-era stuff first aired. There was this great mass of literature by people like Michael Jan Friedman, calling the Klingon homeworld Klinzhai, and a whole heap of speculation about Klingon and Romulan culture. Almost all of it is now defunct, because it was overruled by the new continuity being established.
Check out the Signature Editions of some of the Trek novels to see how things have changed... I particularly recommend "Worlds in Collision" (a collation of two Reeves-Stevenses' novels) and "The Hand of Kahless" (a combination of one by John M Ford, and one by Friedman) as perfect examples of this. They even have forewords by the authors reflecting on the stories after however many years it's been since the novels were published. Extremely informative, they are.
On the subject of the Star Wars EU, frankly I'm OK with them overwriting the novels. It's just a story, no matter how great I think it is, and where the novels take things is different from where the films will, is different from where I would, or you would, or anyone else would. I love reading/hearing about other possible directions for stories - else why would I be reading the old novels?