From Chapter 56:

Bellatrix was still transparent within the Cloak, but to Harry she was no longer hidden, he knew that she was there, as obvious to him as a Thestral.

It would have had to have been a different cloak than Harry's, but then, I guess Hermione did have one on her; it might not have been good enough to hide her from the troll, but perhaps it would have hid her from Harry. And I suppose that obscuring the real Hermione from Harry would make sense under the 'if you want to change the past, you can't know if you've already succeeded' rule, from the end of 76.