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I'm tentative to make predictions here since, reading through comments, I consider you folks more grounded in rationality, logical thinking and also fictional predictions than me. But I wanted to share a thought and get feedback, so here goes.
My interpretation of the big magical release goes like this: Hermione's brain, experiences, knowledge, magical ability, etc., are programmed via the genetic magic marker to upload into... something. The Atlantean Neural Database, or something like that. We've got reason to believe that magic was artificially created and the genetic marker programmed into people, so that they are capable of interfacing with reality on a far more interesting level than most people. We've also got plenty of evidence to suggest that the brain is, if not fully understood by magical knowledge, more than capable of being interacted with. We have Legilimency and Obliviations capable of accessing memory, thoughts, knowledge, and intentions; the author is capable of working with things WE don't know about because wizarding knowledge is stated to have been lost, so we also have some unknown-unknowns working against us. So the odds of neural magic having existed in a more advanced form (peaking in Atlantis) seems pretty decent to me.
If I imagine myself as a group of wizards (or an ultra clever protoMerlin), capable of interacting with time and brains, and I'm still interested in doing research and data gathering, then it seems like being able to collect ALL neural data on ALL wizards would be a big boon in doing research. So the magic marker, given a certain degree of trauma, could trigger the release of information back to the source of magic. Dumbledore's certainty that Hermione is dead (despite certainty in other comments that HP should still be capable of preserving her brain) tells me that he knows, based on that big blast of magical resonance stuff, her death is now as official as it gets. He's also very confident that life goes on after death; if you're capable of uploading every part of your brain that makes you YOU into a big database, there's no reason for him to be wrong, in this sense.
And from a narrative perspective, the fact that Harry immediately jumps to conclusions about Atlantis and searching outside of time to bring her back--no to protect everybody else from death, as was his original statement, but to specifically fetch the string of information that represents Hermione and restore it to existence--suggests they're related.
Maybe I'm late to the party on this idea though. Odds of somebody else thinking of it before, especially if I'm the one thinking about it, seem pretty good.