The more I think about this the more that bit in ch. 48 seems like a mistake by the author. Harry did tell her. She presumably still has the "42" envelope containing the piece of paper where Harry wrote the secret obliquely. Ch. 48 reads like EY forgot that.
Edit: OK, technically Harry implied back then that she should avoid reading it unless she had to, so Hermione followed his wishes when she put the paper away unread. How do they expect this to work?
"That feels like a dementor. Better apparate away -- oops, can't do that, another wizard must have made an anti-apparation hex. Better pull out that wax-sealed paper I always carry and calmly open it with one hand, using the other to hold my wand in case I need it to defend against my postulated wizard opponent, and then calmly read Harry's hint while hoping the dementor doesn't make me forget who Harry is, and then figure out what he meant, and then apply the knowledge to the problem of duplicating a spell that Harry prepared carefully in a relatively safe situation."
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.