Neither Nintendo or Atlus had substantial details on the Fire Emblem/Shin Megami Tensei crossover at E3, but Nintendo designer Hitoshi Yamagami did say the game is on track.
At the end of the presentation of the upcoming Code Name S.T.E.A.M., the question of whether that game was slowing down production on Shin Megami Tensei X Fire Emblem was brought up. Yamagami shook his head and said no, and that the game was moving along on schedule. He followed up saying if he revealed anymore he would probably get fired.
For more on the previously announced crossover, head here.