At this point in time, the arguments are as follows:
Loraan's soul survivalEdit
The first half of this speculation revolves around Loraan's soul not being destroyed by Blackwand, which can be broken down as follows:
Morrolan was mercifulEdit
It may be that Morrolan had told Blackwand not to destroy any souls while he was fighting with Loraan's guards, because he realized that these soldiers were simply doing their duty. When he went up against Loraan himself, the instruction to not destroy souls was still in place.
There might have also been pragmatic considerations involved: If there was any problem with the staff after they retrieved it (such as, for instance, it not being the correct one), it would have made sense to keep Loraan's soul around in case questions needed to be answered.
And perhaps Morrolan just didn't want to destroy Loraan's soul, feeling that it was bad enough that they were breaking in and stealing things.
Blackwand was mercifulEdit
It may be that Blackwand chose not to destroy Loraan's soul. When Vlad was asked about Loraan's survival, one possible interpretation of his response of "Take it up with Morrolan. Or rather with Blackwand" is that perhaps he thinks that the sword might have acted independently. We do have some evidence of Blackwand acting on its own impulse, in protecting Morrolan. Why a Great Weapon might independently choose to not destroy the soul of someone who is attacking its owner is unknown, and may be a fatal flaw in the idea.
Loraan was dead or dyingEdit
Vlad has told us that sticking a Morganti weapon into a corpse will have no effect on the soul, even if the corpse has been freshly killed. Being detached from the body, the soul is protected from eternal destruction.
Vlad killed LoraanEdit
Vlad managed to fling a knife into Loraan's stomach just before Morrolan attacked Loraan with Blackwand. It may be that the knife severed a major artery, and Loraan was rapidly bleeding to death even as Morrolan approached.
Loraan committed suicideEdit
Loraan was a powerful sorceror and necromancer, and presumably was well aware of the above knowledge about souls and Morganti weapons. Once he recognized that he was being attacked by a Great Weapon, he may have decided, in panicked despair, to necromantically eject his soul from his body, rather than allow it to be destroyed. Considering the degree of interest Loraan showed in souls and (arguably) Great Weapons, this is a solid possibility.
Alternatively, Loraan may have had other means to kill himself with, either mundane or sorcerous, and used them to do so, in order to protect his soul.
Protections in placeEdit
Another possibility is that Loraan had some automatic sorcerous/necromantic mechanisms to protect his soul while he was in his keep, which were activated by his approaching death. This could have led to a tug-of-war between Blackwand and these mechanisms, which ended when Morrolan withdrew and fled.
Alternatively, it might be that because Loraan was a wizard, he had bound his soul to his staff, which was the mechanism that protected said soul from destruction.
Loraan was protected by being an undead wizardEdit
This line of thinking, arguably the most tenuous, is that Loraan was undead (and a wizard, of course) even before he was struck by Blackwand, and that this somehow protected his soul, or in some combination with the previous note about protections. (Also, if Loraan was undead, he met at least a one definition of being 'dead' as well)
It should be noted that this theory is the one that Vlad seems to accept when discussing Loraan's condition with Savn in Athyra, which may lend it more credence. As to how exactly Vlad would know about all this is a bit of a mystery, however.
This may seem particularly unlikely because there has been no hint that being undead can protect one from a Great Weapon, and there is the added point that Loraan was killed by a non-Great-Weapon Morganti dagger.
However, it is easy to overlook the mundane impact of contained Dark Water. Something not involved in the Taltos encounter. (If, for example, it required necromanic abilities to allow his soul to retreat to the safety of his staff during the initial enounter with Blackwand, this ability may have been blocked by the Dark Water used by Savn, thereby allowing his soul to be destroyed.)
One side theory of this is that Loraan, despite all appearances at the end of Athyra, was not actually killed by that either, and will return to cause more grief for Vlad and/or Morrolan.
Loraan already has a Great Weapon or is attempting to create oneEdit
Vlad just happens to pick up Spellbreaker in Loraan's sanctum. Not only was Aliera's soul kicking around in a stick in his workshop, proving that Loraan was more than capable of hiding and protecting a soul in this manner, he also possessed one part of another Great Weapon. If he is in fact linked to another Great Weapon, one that is currently not recognized, such as Pathfinder was not, it is a high probability that he was not killed by a lesser Morganti, even with the Water as a factor.
Alternatively, he was in the process of creating one using Aliera's soul. We now understand that a soul is required to animate a Great Weapon with personality, intelligence, and other qualities. The person who is sacrificed, willingly or not, determines in some part the abilities of the Weapon. In using Spellbreaker and bonding it with Aliera's soul, possibly even knowing her Divine origins, he would have had a Weapon of predicable and powerful capabilities, including that of Elder sorcery or Chaos affinity. It argues that Sethra knew this, as she hired Vlad to recover the soul, rather than wait to deal with it herself when she could leave Dzur Mountain. We get the impression of extreme haste, especially for Draegarens. As Aleira has been missing since the Disaster, what else could possibly make her recovery so urgent, other than the need to preserve her soul from becoming an immediate experiment?
Loraan's researches in this area would certainly have given him an edge in dealing with another Great Weapon, and he may have even taken precautions against this well before he began, enabling him to survive an attack by Blackwand, particularly if he anticipated a rescue attempt...
Assuming that one of the above scenarios is correct, there remains now the question of how Loraan returned in Athyra as an undead.
He was already undeadEdit
If you agree with this line of thought, there is no need for any of the following justifications. He was undead before, he didn't die, his soul wasn't destroyed, so he stuck around.
If you disagree with this line of thought, it is probably because you have no evidence that he was undead in Taltos. Considering how limited the contact between Vlad & Loraan, or Loiosh & Loraan, or a dog & Loraan, was in Taltos, this isn't surprising.
If Loraan did manage to evade Blackwand's destructive power by using sorcery or necromancy, it may be that this method nevertheless damaged Loraan's soul, such that Loraan could only be revivified as an undead. In particular, Loraan being in the process of dying (rather than already completely dead) might have meant that Blackwand could gain enough access to his soul to damage it.
Escape from the Paths of the DeadEdit
If Loraan's soul was somehow intact despite Blackwand, he may have been permitted to leave the Halls of Judgment by the Lords of Judgment for some unknown reason.
Considering his past actions, this could be hard to justify (although the reason might have been for him to do some sort of penance for his past actions).
Alternatively, given that the gods are somewhat lazy and apathetic: If Loraan managed to avoid coming to their attention, he might have left the Paths of the Dead as an undead without them ever noticing, or if they noticed, without bothering to stop him or warn anyone.
A side theory that follows from this is that Loraan may have been allowed to leave by Verra, precisely so that Vlad would meet up with him during Athyra. Whatever the explanation for Loraan's departure from the Paths, it seems likely that Verra may have inspired Vlad to go to Smallcliff, later. This may have been either to season Vlad after letting Loraan go, or perhaps just as her method of dealing with Loraan's undesired escape.
Given that Verra seems to have plans for Vlad, this may have been part of preparing him for whatever task lies in store for him.
Still another possibility is that one or more of the other gods facilitated Loraan's return in secret, for his/her/its own reasons. It has been hinted that at least some of the gods may have originally been Jenoine, transformed by the energies of the calamity that produced the Greater Sea of Chaos: might such gods retain an affinity for their mortal fellows, and subvert the aims of the non-Jenoine Lords of Judgement in that race's favor?
Something just went wrongEdit
Another possibility is that Loraan was not destroyed by Morrolan specifically because Morrolan knew of, or suspected, Loraan's involvement with the Jenoine, and he wished to make sure that Loraan's soul could be interrogated at some point (perhaps by the Necromancer, or the Lords of Judgement), and ordered Blackwand to simply "hold on" to Loraan's soul.
Perhaps the various events in the Paths of the Dead may have involved Blackwand's releasing Loraan's soul at some point, either deliberately or accidentally.
At this point, Loraan may have been interrogated by the Gods, and permitted to return to the world of the living as an undead so as to perform some task for them (see above), or he may have simply escaped.
It may be that he wandered the Planes of Existence until he found Tri'nagore, who might have felt that they had sufficient common cause that he (Tri'nagore) would help Loraan by returning his soul to his body - but since too much time would have passed, only as an undead.