If Balduran was to be ressurrected, it would be as a separate entity from the mind flayer. Withers explains that Mind Flayers don't have souls and that the soul vanishes when a host is transformed. It is uncertain if this means destroyed or moved on to the afterlife. If the latter, a sufficiently powerful Cleric might've been able to ressurect pre-transformation Balduran, but Mind Flayer Balduran can't be cured that way because it has no soul.
If the Emperor has no soul, then it is possible that Balduran and the Emperor can exist at the same time - paradox
In the ending where Gale is the Mind Flayer, there is an option to ask Mystra to take Gale's soul to Elysium.
At the same time, it is clearly visible that the soul flies out of the Mind Flayer, but at the same time he remains alive.
The soul is self-awareness as a person? Soulless illithids obey the Elder Brain, and have no individuality. Individuality is the soul?
Could the Emperor be the exception, preserving Balduran's soul? He is an independent individual, has Balduran's personality, his memories, and identifies himself as Balduran, could this be the same person whose soul for some reason was not destroyed in the process of cerebromorphosis