Loki is in her (I can't remember if she/he had any pronoun preferences or even thought like that at this point in the fic) female form, on a couch in Avenger's Tower with Tony. As far as I remember, she only takes on a female form with Tony, and even then only rarely. Natasha, I think (or possibly Bruce), walks in on them, seeing Loki as female for the first time, and simply asks what pronoun she prefers. Which is the point that Loki realizes that there are others like her (Asgard not being a very accepting place?). Loki is a bit shocked but happy.
Trouble is: as far as I remember this is only a scene in a larger story, which is not focused on this. I'm pretty sure it was Tony/Loki and that it was Natasha that walked in on them. Loki did not know that there were others like her/him who did not feel comfortable being simply male/female, or had doubts about their gender identity. Or that there even existed a pronoun for those that felt like neither. As far as I remember the Avengers were pretty nonjudgmental - can't remember what Thor thought.
I'd wager that this was a long fic, possibly 100 000 words or more, where this was a smaller theme, but the main point was probably fighting a bigger enemy or a Loki-redemption arch. It's probably at least a year old, likely more.
I've tried searching on AO3, but this isn't a small fandom and it doesn't help that I'm pretty sure the genderfluidity wasn't the point of the fic.