Loki'll be male again next chapter, and he remains thus for the next two chapters, then goes female for the last chapter. And he starts out the sequel male. (Yes, sequel. I think I mentioned it in the A/N of the first chapter, but I'm not certain. I'm still working on chapter one of Rough Edges, though. But I'm writing again, and if Tony stops being difficult, I shouldn't get hung up again. *swats Tony*)
The only way that Loki's gender is at all important to the plot is that Male!Loki can't really be seen outside Avengers Tower and SHIELD installations, but Female!Loki can. The sex, when it happens, will be with Male!Loki. In case that was a concern...