<p>@Seel, considering Kaguya wants back all chakra, I suppose chakras of those who have died still has to be around for that to work. If it is anything like energy, then it can't be destroyed, it only takes on another form.
@Ulti, Kushina was in the afterlife all along since shortly after Kurama's claw struck her. Naruto didn't meet her soul, only her chakra. There was no part of Minato in the afterlife as well, ever.
</p>