I wrote a short story on this once, and used it as the basis of several other concepts.
Here was my way of justifying it - souls were simply patterns of 'creation' - anything that was arranged in a certain way was deemed to be at one with 'creation', or in other words, god.
So souls were pieces of god torn away. When a person died, they slowly moved through the tiers of creation (angel, arch-angel, etc.) until they lost all individuality and became one with creation again. Every now and then this didn't work as it should have, and a soul was returned.
In other words, souls were like 'water' - sometimes they were part of the ocean, and sometimes individual drops of rain. Water is never created or destroyed. Neither were souls.
Mind you, this was simply a spec' fiction idea, and exists only in my twisted mind.
Athon