The ministry of Joseph Smith fortunately replaced many, but not all, of the plain and precious parts of the Bible which were taken away. His retranslation of the Bible restored great truths, especially about the events written in Genesis. This is seen in the entire book of Moses and the Joseph Smith Translation of Genesis, especially chapter 50.
The historical events surrounding the creation of the New Testament record are poorly recorded. No single person or group has been attributed with the compilation of the Bible as we know it and the year that it was put together is still in dispute. Therefore, external evidence corroborating Nephi's claim is lacking. This in no way takes away from the truthfulness of his statement. There is evidence, however, that epistles of early church leaders were evaluated at different times and judgments were made as to whether they should be included as canon or not. Some of these works were probably spurious, but others were probably inspired. The historical record is complete enough to list some of these works and the confusion which at times prevailed over what records should be included in the New Testament. A historian of the 18th century named Mosheim recorded:
"As to the time when and the persons by whom, the books of the New Testament were collected into one volume, there are various opinions, or rather conjectures, of the learned; for the subject is attended with great and almost inexplicable difficulties to us of these latter times. It must sufficed to know, that before the middle of the second century, most of the books composing the New Testament were in every Christian Church throughout the known world, and were read and regarded as the divine rule of faith and practice.
"…Not long after the Saviour's ascension, various histories of his life and doctrines full of impositions and fables were composed by persons of no bad intentions perhaps, but who were superstitious, simple, and addicted to pious frauds; and afterwards various spurious writings were palmed upon the world, inscribed with the names of the holy apostles. These worthless productions would have wrought great confusion, and would have rendered both the history and the religion of Christ uncertain, had not the rulers of churches seasonably interposed, and caused the books which were truly divine and which came from apostolic hands, to be speedily separated from that mass of trash into a volume by themselves." (Mosheim's Ecclesiastical History, 6th ed., 1868, pp. 36-39)
In light of Nephi's statement, one can't help but wonder if the works which are referred to by Mosheim as "spurious writings…worthless productions…mass of trash" weren't in actuality, "plain and precious." Here we see evidence that the "rulers of churches" interceded to decide what should be included and what should be excluded. Mosheim next chronicles a series of these other works which were excluded. They include the works of Clement, a bishop at Antioch and companion of the early elders of the church, the Epistle of Polycarp, who had direct contact with John, the Revelator, the Epistle of Barnabas, the Shepherd of Hermas, and many others.
James E. Talmage recorded the importance of councils held later to determine what should be included as canon:
"In addition to individual testimony we have that of ecclesiastical councils and official bodies, by whom the question of authenticity [of the books of the New Testament] was tried and decided. In this connection may be mentioned the Council of Nice, 325 A.D.; the Council of Laodicea, 363 A.D.; the Council of Hippo, 393 A.D.; the third and the sixth Councils of Carthage, 397 and 419 A.D.
"Since the date last named, no dispute as to the authenticity of the New Testament has claimed much attention. The present is too late a time and the separating distance too vast to encourage the reopening of the question. The New Testament must be accepted for what it claims to be; and though, perhaps, many precious parts have been suppressed or lost, while some corruptions of the texts may have crept in, and errors have been inadvertently introduced through the incapacity of translators, the volume as a whole must be admitted as authentic and credible, and as an essential part of the Holy Scriptures." (A Study of the Articles of Faith, James E. Talmage, p. 248)