Nefernefrure ceases to be mentioned after year 14, and is not shown in the mourning scene at the death of Meketaten (niether is her little sister, Setepenre), and many conclude from this evidence that she predeceased Meketaten. But there really is no way to know for sure.
Some have, like with Nefernefruaten ta-Sherit, theorized that Nefernefrure was sent away to marry a foriegn king, but this was not done in Egypt. Foreign princesses came into the country, but there is no documentation of any Egyptian princesses leaving. In fact, Amenhotep III (the Amarna Princesses' grandfather) told one foriegn king that it was never done when he asked to marry an Egyptian Princess. So it seems rather unlikely that any of the Amarna princesses were sent off to be wed to a foriegn king.