Evey now and then when running SR, I’ll run into the same map I had on a run before and there will be Shattered Souls lying on the ground from the run I did before.
Now, in the specific instance where I had it happen just now, I think I can pinpoint the cause. The map I was on was one I failed to complete previously. I got nuked by a Nemesis at 79, didn’t go back, told Mazaan to close the portal and two runs later I got the same map, and at the spot where the Nemesis was that killed me was a Celestial Shattered Soul. So it seems that if I don’t complete the run and just close the portal, the game will kill the enemies on that map, drop the Souls but won’t wipe the souls for the next run.