It is said in the previous life she was princess Amba. If for that reason Amba was a woman, then the question arises, is the gender of soul fixed or soul has no such restrictions? More than what is written in Mahabharata, I am looking for logic.
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I am yet to research about authenticate stories about shrikhandi but here is an answer about soul.
No, the self doesn't have gender, it's just a body which has gender.
According to Shwetashwatara Upanishad:
V-10: He is neither female, nor male, nor neuter. Whatever body he assumes, he becomes identified with that.
Another translation from Vidyaprakash:
The Jiva is not female, nor male nor neuter. Whatever body it assumes, it becomes filled with that body.
It's also recommended to forget such things in the path of Yoga by Swami Vivekananda on his work Rajayoga:
Agreed, soul has no gender. It takes the gender of the body it occupy. The question is, will a female in next birth will always be female of that species or it can of different sex. This is relevant in case of Shikandi as Bhisam treated Shikandi female because in previous life she was Amba, a female.