She needs a nomination to go to an Academy. AFA gave an LOA so they want her. There are nom sources through AFA if she doesn't get one the usual way but AFA has to choose to use it on her vs someone else (lots of these go to the prep school or athletes). They have limited number of supe noms but they are not required to use them on LOA's. I have heard stories of an Academy calling a MOC office after the slates are set asking that the MOC consider giving a nom to someone if they had room on their slate (if they didn't give a full slate of 10 - some MOC's only nominate as many as they feel are good candidates so there could be room on a slate). If the slate is full then it is more difficult.
Having 2 noms to Navy gives flexibility to USNA and thus should be helpful. I have heard of kids with an LOA to their 2nd choice calling the 1st choice and asking their admissions rep what they can do to make their file more competitive & mentioning the LOA in the conversation. Letting USNA know about an LOA but that Navy is first choice etc.... I have heard of kids getting an offer to first choice shortly thereafter (since they have a nom), not necessarily because they got an LOA someplace else but rather that they got their file looked at. Also, be certain she updates her file at USNA with anything additional, another honor or if her team won something, whatever.
Is your D an athlete? If so, she should contact coach. If USNA is truly her first choice update the file .... call admissions and be sure she expresses her deep desire etc...
It is possible to get a supe nom and who knows, maybe AFA will use one on her. Or, did she apply for VP nom? The Academy decides who gets the VP noms so maybe they'd give it to her. It depends on how badly they want her. Obviously they want her or she wouldn't have gotten the LOA. Depends on how many supe/VP/other noms they need to use on prep kids and any others in your D's situation.
Good luck and let us know how it works out.