Via Pat, R. Scott Bakker has confirmed that he has almost completed The Unholy Consult, the concluding volume of The Aspect-Emperor Trilogy and the sixth book overall in the Second Apocalypse series. He's working on the last two chapters of the first draft now. However, the book has gotten quite large and the rewrites are apparently going to be fairly involved, so it is still impossible to project a publication date.
Just heard back from Scott this afternoon. He says he's labouring on the final two chapters of TUC and that the book is getting ridiculously big. And at this point, he has no sense of what the rewrite will entail.