My first thought was that she’d been transfigured into the pajamas, but I don’t think that’s likely. My theory is that when Harry slept in his bed it was the second time he’d been through that time period. The first time, he stayed invisible with transfigured Hermione in his possession, waited until woken-up Harry had finished being searched, gave her to woken-up Harry, then went back in time and went to bed.
That would require him to stay up all night, since he cannot know in advance the exact time Flitwick will arrive. It is much more likely that the Harry we saw was the first one, and that he’s now going to go back in time to pick up the body.
My first thought was that she’d been transfigured into the pajamas, but I don’t think that’s likely. My theory is that when Harry slept in his bed it was the second time he’d been through that time period. The first time, he stayed invisible with transfigured Hermione in his possession, waited until woken-up Harry had finished being searched, gave her to woken-up Harry, then went back in time and went to bed.
That would require him to stay up all night, since he cannot know in advance the exact time Flitwick will arrive. It is much more likely that the Harry we saw was the first one, and that he’s now going to go back in time to pick up the body.