The sentence "Time..." is in response to a question from Hermione about how H&C knows Harry will turn dark and destroy her, not in regards to anything having to do with the conversation itself.
Also if you reread the passage in question, you'll see several hints that indicate a long time passed for Hermione also, even though she didn't remember it, e.g. *"Her hand was almost slipping on her wand, there was a sense of fatigue in her fingers like she'd been holding the wand for hours instead of minutes", and ofcourse the fact that the rush of adrenaline at the beginning of the conversations corresponds to the rush of fear at H&C decloaking at the end.
(The HPMOR discussion thread after this one is here.)
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. There haven't been any chapters recently, but it looks like there are a bunch in the pipeline and the old thread is nearing 700 comments. The latest chapter as of 7th March 2012 is Ch. 77.
There is now 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.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven, eight, nine.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: