Re-reading the story, I see a lot of evidence that Dumbledore didn't know that Quirrell was Voldemort. For example, Chapter 62:
You are no longer taking lunches in Diagon Alley, even with Professor Quirrell to watch you. Your blood is the second requisite Voldemort needs to rise as strong as before.
He refers to the same issue when talking to Bones. It would make no sense for him to do so if he believed that Voldemort had constant access to Harry and countless opportunities to "accidentally" obtain his blood (as indeed happened with the newspaper).
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 117.
Plans for next chapter release:
There is a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)