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I feel like, assuming that was on the Emperor's to-do list at all, it was probably low on the list with a note reading, "Figure it out later," next to it.
Humans seem to still be a fair ways off from becoming a species of powerful psykers. Lots of things could change before they go to that point. Spitballing possible solutions:
* If the Emprah intendned to weaken/kill the chaos gods somehow, then this would become kind of a non-issue. Eldar souls used to hang out in the warp after death before reincarnating. In a sufficiently chill warp, humans could maybe do something similar. Or just hang out indefinitely.
* The imperium already has a certain amount of brain-in-a-jar tech. I guess you could probably transfer a psyker's mind/soul into a slightly fancier servo skull and just make all your psykers functionally immortal.
* Exodites manage to get their souls sucked into their world circuits without using spirit stones as a medium. Humanity could probably adopt something similar. They were planning on ripping off the webway, after all, so ripping off world circuits should be within the realm of possibility.
* Maybe the Emprah just intended to absorb/unite with all the dead human psykers. Compare to Cegorach absorbing the souls of his harlequins when they die. Some lore says the Emprah is already a gestalt soul, so adding to that gestalt or smooshing the newly dead into their own gestalt beings might not seem unreasonable to him.
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