None of the books of Nephi in the Book of Mormon were originally designated by number. Each was the book of Nephi, and distinguished in the title with the genealogy. Thus, what we have typeset as a header may have been part of the intended title, at least up to the description of Nephi as “one of the disciples of Jesus Christ.” The final sentence is probably the header proper.
Because we have four books of Nephi, and we know of three Nephi’s (son of Lehi, son of Helaman, and son of Nephi who was the son of Helaman), it has been assumed that this new book must indicate yet another Nephi. There is no evidence for a Nephi, son of Nephi, son of Nephi, son of Helaman. The title of the book clearly indicates two things: 1) this Nephi is the son of Nephi; and 2) this Nephi is one of the disciples.
It is that last designation that helps us understand that the Nephi whose name is used for this book is the same as the one from whose personal record the book of 3 Nephi was taken. Further evidence is in the first verse of the book, which indicates: “the thirty and fourth year passed away, and also the thirty and fifth, and behold the disciples of Jesus had formed a church of Christ in all the lands round about.” Thus, the book of 4 Nephi begins soon after the end of the book of 3 Nephi, and not enough time later to suggest that the Nephi (who appears to have been the head of the twelve disciples) would have passed away.
Why then a different book? There are two reasons. The first is that the book of 3 Nephi was taken from Nephi’s personal record, with some backup in the early chapters from the large plates. In 4 Nephi, we are getting Mormon’s severe condensation of Nephite history. The passage of time is noted in a way that echoes the annalistic format of the large plates.
When the book of 3 Nephi began, Nephi had the large plate record, and he was the record keeper. He kept the record of the previous dynasty, to which he did not belong. The Nephite nation had been destroyed prior to the arrival of the Savior in Bountiful. Nevertheless, the large plates were in Nephi’s possession.
In 4 Nephi, we have a reconstitution of the Nephite people as a nation. While it does not clearly state that Nephi, son of Nephi, had become their ruler, it is a logical inference from his position among the twelve, his possession of the records, and the fact that 4 Nephi bears his name. Thus, 3 Nephi was a book outside of the large plate record, and 4 Nephi returns to the large plates with a new dynasty, and, therefore, a new book name.