As a refresher, Misfile was about a "misfile" by a stoner slacker angel that caused two minor reality changes. A guy ended up getting refiled as a girl, and another girl got refiled as being 2 years younger. So starts off largely as a little gender bender fare, but it does became quite apparent that this is all actually the thinnest allegory for gender dysphoria, as the main character is frequent to remind us and the characters in the know, that he is a man trapped in a woman's body. There were interesting avenues it could have taken, particularly in how his friend ended up getting to use her two regained years to better her life, improving her relationship with her mother, finding new friends, and learning more about herself and what she wanted to do with her life. This could have left a more significant point of contention where "fixing" the misfile would give the MC his dick back, but at the cost of her quality of life being significantly impacted.
Perhaps the MC would learn to deal with his new body, at least for her sake?
But the author has written about his own father came out as transgendered, and then committed suicide as a result, so it very quickly became apparent that a lot of this story had become a sort of self-help therapy session. Naturally, everyone got everything they wanted, and everyone was happy, the end.