The Nature of the Soul and Ki

Manifestation

The soul and ki are two layers of the same idea referred to as "conciousness". All living things have a conciousness, though it manifests in a multitude of ways. On top is the layer of the soul, the link that binds it to the outer planes that provides the positive energy for life. Below the soul is the ki, the layer that accounts for the physical interaction between the soul and the material world.
A tree, for instance, has a ki that ensures its energy is directed towards its function as a tree. Should that tree's ki become severed or corrupted, it slowly blights and dies. For a creature like a deer it is much the same, as long as the ki remains unchanged, a deer remains a deer.  A corrupted deer is no longer able to function as a deer would, and the soul is incapable of remaining for long without the right ki.
Where complexity begins is in those beings whose soul and ki ensure for complex moralities, emotions, language, etc. The first concept to understand is that reincarnation is real on this material plane. However, it is not an automatic process or natural law. A soul that is deemed needing more time on the prime material can be brought back, its ki forming around the entity in which it is bonded. The longer it has been from time of death to its attempted resurrection makes a massive difference in the amount of effort required.
There are afterlives for souls, but those are places for those souls that have proven ready for them by judgement of Thuses, or that are prevented from them. A soul can ask of Thuses for another chance, and that is when reincarnation comes into play. Thuses can grant the soul another chance, but never guarantees the form the soul takes, and rarely offers third chances. A soul is prevented from entering the afterlife when it is dedicated to the Old Gods, no afterlife can claim such a tainted soul, and that soul is banished to the Far Realm, where it will likely become an aberration.
The second concept is that ki is responsive and reactive, based on the physical world. It does not control the form it inhabits, but the form can control it, and mastering the art of manipulating ki can be peaceful or destructive, but always inspiring awe. How the ki is treated changes what happens to the soul when the time comes for death.
The question becomes, how does magic affect this?  Just as everyday actions affect the ki in both positive and negative aspects so too does magic. Healing magic utilizes positive energy to heal the body and soul through its ki.
Necromancy corrupts the ki, and utilizes negative energy to destroy, control, and manipulate the body and soul. Even resurrection is not positive, as the natural order is for a soul to leave the material plane once separated from the ki and body. That does not mean that it is not done, but it is not natural. The process of resurrection requires the petitioner to come before Zindraaldein and commune with them about a particular soul, bringing a case before them to bring them back to the living. This is not always granted, as some souls must move on, and have an equal say in whether they desire to return or wish to move on to their afterlife.
Transmutation is separate in that it changes form, but does not change the ki or soul. This does not make it positive, since the new form is not the same as the old form, the ki is not compatible with the new form, which affects the very fabric of what that life is and was. This is why powerful magic is necessary to change a form in a permenant fashion. In that same vein, the magic required to make such transformations permenant is so great that it changes the very ki of the soul to match the form, and there are those of the celestial host who find this kind of manipulation antithetical to their domains.
Consider also the significance of the soul. Creatures outside the Prime Material do not have souls, it is both a blessing and a curse for mortal-kind to have them. The gods need souls, so their hosts work to ensure that mortals are dedicated to their domains, and often come into conflict over a soul. In what a mortal places their worship, dedicates their lives, drives where their soul belongs. It does not even have to be an active process, for the gods are watching and can read the soul and know its deepest truth. Worship of the god of war is conflict, a desire to conquer, a thirst for battle. The god of war needs not hear its name called out to know a mortal worships them. On top of all of this is the soul trade, a scheme that Raxas developed where the Night Hags and those that serve them could trade in souls that did not reach the afterlife or were prevented from moving on at all. Zindraaldein the Soul Herald despises the soul trade, and makes all effort he can to ensure the dead find their proper place.

Type

Metaphysical, Divine