If a soul is reincarnated in different bodies, in which one does it return to in the time of Moshiach?
First, though, we need to explain why a soul is reincarnated into another body in the first place.
A soul is reincarnated when it did not accomplish all of its obligations during its stay in a specific body. The person may have completed his particular mission on this world; however the soul has to complete all of the 613 commandments in order to achieve completion for all its 613 components. Thus the soul descends once again to finish the task.
Every body which was inhabited by the soul assisted the soul in the fulfillment of its mission. Those components of the soul which were rectified through the mitzvot fulfilled by a particular body always maintain a connection with that body, and will return to that body to revive it with the Resurrection of the Dead. In short this means that souls will be divided into different bodies.
How is that possible, you may be wondering? The Divine soul is a reflection of its infinite source, G‑d Himself, and thus has the ability to vivify any number of bodies. In fact, according to the mystics' teachings, the entire soul of a person is never "clothed" in its body. Only a ray of the soul descends into the body, for otherwise the body would be completely overwhelmed by the soul's brilliant intensity.
Refer to the following links for more information on these topics:
Moshiach and the Redemption