According to the UFC website, Lyoto Machida has been removed entirely from the UFC 89 card. Shane Carwin's fight is now on the main card instead.
I haven't heard any estimates on how long Thiago Silva will be out, but this could be a blessing in disguise for Machida. Beating Thiago probably would not have put him into title contention, and he's now open to a face a number of different guys.
One name being thrown around is Mauricio "Shogun" Rua in December. Shogun would be an underdog in that fight, which would have been hard to believe back before their respective fights at UFC 76. It's hard to see how Shogun would beat Machida stylistically, but it makes for an intriguing fight.
Personally, I'd like to see Machida fight Rampage Jackson. That is the true number one contender match at this point, and with Chuck Liddell out of the 205 title picture, it's much harder to keep Machida in title purgatory. Machida/Shogun is more like a Sherdog dream match and less of a match that will do much of anything for either guy.