In a recent interview with US Gamer, Fire Emblem Fates‘ producer Masahiro Higuchi discussed the difficulties of making two games at once. He claims that making one game presents enough challenge, so working on two projects simultaneously was certainly difficult. However, thanks to developer Intelligent Systems being a veteran studio, the project was manageable, as Fates‘ main staff “has been more or less similar to those who worked on previous games.” Also, as Birthright and Conquest utilize the same assets, it allowed for a single team to work on the core of both games. Separate teams then worked on specific level design. In total, around 150 people are employed at Intelligent Systems, making the development of the two games an achievable feat.
Source: US Gamer