When Nephi and Lehi begin their missionary journey, they begin in Bountiful, and then head south. Although Mormon had told us that the Nephites had lost most of their territory, his readers had to remember that this would have included the loss of what had previously been their capital city. Verse 16 drives that home when we learn that Nephi and Lehi enter “the land of Zarahemla, among the Lamanites.” In the interim, Bountiful may have, at least temporarily, been established as the new center city.
Even though the recapture of Zarahemla appears to make it again the seat of the Nephites prior to Christ’s birth, when the destruction comes at Christ’s death, the risen Lord appears in Bountiful and Zarahemla, which takes fire (3 Nephi 9:3). The function of the seat of government appears to move north, most likely to Bountiful, after that time.