This scenario is interesting and good news for your daughter. As you probably already anticipate, she must complete the entire USMA application process to finalize the USMAPS 'appointment.' Clearly, to be eligible for a USMA appointment this year, she must also apply for and receive a nomination. Point is that she must complete the entire process, and she can still earn an appointment. As noted, at least she has the USMAPS invitation in hand now. I happened to have two student there now.
One important point that I note routinely for the CFA: I tell all of my students that the CFA is a 'beginning' not an end. Your daughter should commit to her 'best fitness' as a military officer candidate. Her workout routines should be 'routine' and continue throughout the school year and summer as she prepares to arrive at the Academy, or the Prep School, ready to meet the fitness requirements for either program, USMA or USMAPS.