Okay, here's all that I know. IMDB no longer has the new film listed. This means it's not in production yet, but the movie website is still up. The author recently published a sequel short story and they're still fighting him over royalties from DVD sales of The Last Unicorn, so that could be holding things up.
But I found this in one of his interviews in 2006:
"I can't talk much about it yet, but there seem to be all sorts of possibilities in the works — real possibilities, as opposed to your usual written-in-sand movie possibilities. I do think we might be able to resolve this issue, and also that a live-action Last Unicorn has a good chance of happening."
:D