Probably from your daughter’s standpoint, her godmother’s defection from the Catholic Church isn’t going to matter all that much. Since you’ve posted this in the Traditional Catholicism forum, there are doubtless many other women who can serve as role models and mentors to her.
Many children experience the loss of godparents in other ways: My own godmother died when I was eleven years old. My mother, on the other hand, though slowed down a little by diabetes and arthritis, remains hale and hearty and sharp as a tack (and just as tough as) at the age of 89. So she was always around to make sure I was being brought up as a Catholic, such as she was, which was primarily cultural. The Sisters at school, especially in the late grades and in my high school. were the ones who really ensured my development as a Catholic. I could tell you a story about how three of the Sisters in my high school took a great interest in me and even helped me further my career, but that is all beside the point.
You don’t have to let your parish priest, or the priest from wherever your daughter was baptized, know about this. As others have mentioned, the baptismal certificate is a historical document, only capturing what happened at the time of the baptism, much like a snapshot.
Since the required role of a godparent is to take an interest in the development and education of a godchild in the Faith, and assure the education of a child in the Catholic Church’s teachings if the parents become incapacitated to do so, you might want to cultivate some relationships with other Catholic women to assess their commitment to the Faith. When you find someone whose interaction “gels” with your daughter, and whose commitment to the Catholic Church’s teachings you admire, you might want to privately explain the situation and ask this lady if she would be willing to step into a de facto godparent role.
But there is no “official” documentation required.
BTW–I"m a tremendous fan of Catholic education: I owe who I am today, both temporally and spiritually, a tremendous debt to the Sisters of St. Mary of Namur, the Felician Sisters, the Grey Nuns of the Sacred Heart, and the Fathers of the Society of Jesus.