Upon reading these past few chapters I think that Harry has invented a spell to download Hermiones brain state just before her death and this is what we are seeing with the whole soul explosion when she dies.
We have never seen this happen so far at all in HPMOR, and I would think if this is a common thing then when Dumbledore is trying to prove to Harry the existence of souls this is the evidence he would use to try and prove it to him. The fact that he did not and this only seems to have happened during this one particular incident suggests to me there is something going on.
Also it's been completely sidestepped afterwards Harry doesn't ask dumble does anything about it this chapter when speaking about Godric's sword which he would do if he didnt know anything about it. Dumbledore doesn't mention it because he doesn't know as he appeared after and he sent back instruments in time he didnt go himself so they didnt pick it up.
And when Harry is sitting outside the room with Hermione in there is a big paragraph where he ponders why magic works the way it does and why it requires a wand. This feels really out of place and I think is there to show Harry's thought process in making this discovery.
Fair point, I missed that bit. There goes my theory then