The first phase of colour correction is done first. Just a basic pass. It is then broken down shot by shot and tweaked and then the work starts on it. Colour tweaks can also be done once the shot is finished so everything matches as close as possible. When you're using a lossless codec, the amount of times you re-render something isn't really an issue. Once all the video work is completed, the complete film is rendered to a new video track and work on the audio begins.
On another note, it seems a new fan edit is causing me all sorts of headaches...
http://fanedit.org/ifdb/component/content/article/79-fanedit-listings/fanfix/938-star-wars-episode-i-return-of-the-sith-revisited-edition
I'm getting numerous messages and emails from people asking me where they can get the edit, why have i done episode 1 before finishing ESB:R, etc etc. I guess they didn't bother to check the editors name before bombarding me with all these questions. lol