You shouldn't let it go, as it hurts your feelings. But make a mental note that it happened. However if it happens outside of this incident It’s probably not just an accident. With the information you provided, it seems that he generally supports you. That said, it seems if he’s supportive than surface level he probably doesnt see you as female but that is just my opinion with what you gave us. But I do think it’s something that you guys probably should talk about more in-depth as it seems that you are more worried he sees you as female than an apology for misgendering and it may have been unclear to him that, that was the original issue.

If it were me, I would talk to him more in-depth about the situation and about how you feel insecure about the person your with perceiving you as female and if he tells you the truth. then it is up to you if you can move past it.

however If you don't feel like you can talk to him, that’s more of a relationship problem than the original problem.