Fear not. The re-implementation will be completely backwards compatible. It just a smoother compilation pipeline, and adds some output configurability. But regardless, Jeremy and I have decided it would be best to change the name.
The names I suggested were "CoffeeScript: Reloaded", "CoffeeScript Episode II: Attack of the Clones", "The CoffeeScript Supremacy", and "Live Free or CoffeeScript Hard". Technically, right now it's "CoffeeScript II: The Wrath of Khan". Jeremy suggested CoffeeScript Redux. That's probably the best choice, though a little boring.
Maybe a name that distinguishes this compiler for CoffeeScript from CoffeeScript-the-language would be better? There may be other CoffeeScript compilers int the future, should they really all have the same name and be numbered? "CoffeeScript 2" (or any whimsical name that contains "CoffeeScript") would be confusing, it implies that it's the second version of the original CoffeeScript compiler, which it isn't.
I would be surprised if he didn't have Ashkenas's blessing on the name, since he's been the second biggest contributor to the main CoffeeScript project.
I feel that it implies that it's an official project, but it's actually a re-implementation and separate project.
And if they're not backwards compatible it could lead to a ton of confusion and a fragmented language.
I think if you want your own project then you should at the very least get your own name.