A Neshama is not an object that we can ask if it is here how can it be there.
There are different aspects and levels to a Neshama.
Gilgul can mean different things and is a deeper topic.
If R”L the Neshama in question didn’t come to its place then we are Davenning that it get closer to its Tikkun Hashalem.
If the Niftar has enough Zechusim then they can intercede on the behalf of the living.