Question: What about the extra books? Why aren’t they part of the Protestant Bible? And what about the so called, “Lost Books” of the Bible?
Answer: The Apocrypha were the extra books added to the Bible by the Catholic Church. This set of books was written between the 3rd century B.C. and the first century A.D. They were never accepted by the Jews as Scripture and are not included in the Hebrew Bible (Old Testament). Even though the New Testament may allude to some of them they are never called the Word of God. No apocryphal book claimed to be inspired.
The Apocrypha was officially added to the Catholic Bible at the Council of Trent in 1596. It is interesting to note these books were added 29 years after Martin Luther challenged the Catholic Church to come up with Biblical support of their doctrines of salvation by works and praying for the dead. The doctrine of salvation by works is soundly refuted in the Bible by the Apostle Paul in Galatians and Romans. The doctrine of praying for the dead was never mentioned in the Bible.
The passages from the Apocrypha the Catholic Church used to answer Luther were 2 Maccabees 12:45-46 and Tobit 12:9. They added these books and others so that they would be considered Scripture and support their unbiblical doctrines. We read in 2 Macc. 12:44-45 (NJB), “For had he not expected the fallen to rise again, it would have been superfluous and foolish to pray for the dead,  whereas if he had in view the splendid recompense reserved for those who make a pious end, the thought was holy and devout. Hence, he had this expiatory sacrifice offered for the dead, so that they might be released from their sin.” We find here a description of a so-called event and no command to pray for the dead. Since the Apocrypha was rejected by the early church, the Protestant Bible does not consider them Scripture and are not part of the canon.
Concerning the issue of faith and works we read Tobit 12:9 (NJB) “Almsgiving saves from death and purges every kind of sin. Those who give alms have their fill of days.” Here we see from the Apocrypha a justification for giving to the Catholic Church to rid oneself of sin. This clearly contradicts the teachings of the Bible. The Apostle Paul writes against saving works in Ephesians 2:8-9 “For by grace you have been saved through faith; and that not of yourselves, it is the gift of God; 9 not as a result of works, so that no one may boast.” If giving alms could purge sin then a person could boast I can save myself. Paul says no one can boast because we are saved by faith alone.
Secondly, there are no lost books of the Bible. If the Bible is a supernatural book do you think God could lose a book? Even for the sake of argument, if it is a man-made book, then the Christians who made the decision to accept these books had the authority to do so. It was their religion and what books belonged and which ones didn’t was up to them. Rejected books do not qualify as “Lost Books.”
What standard did the early church utilize to measure which books would be included in the canon and would eventually be called the Bible? Canon means measuring rod, and it signifies a standard that all scriptural books must meet. We believe the Holy Spirit not only inspired the content of the writings but also what books qualified to be part of the canon of scripture. It was the job of the early church to discover what books God inspired. Some of those tests were: 1) Was it written by a prophet of God? (Scripture is only written by men of God); 2) Was the writer confirmed by an act of God? (Miraculous confirmation); 3) Does it tell the truth about God? (Cannot contradict); 4) Does it have the power of God? (Life transformation); and 5) Was it accepted by the people of God? (Quoted by others as from God, called scripture, or received as God’s Word). 
With years of study and discussion eventually 66 books were accepted by the early church fathers as the Bible. A few books were challenged for years but eventually added as part of the official canon of Scripture. At the end of the process the books that were accepted were received by all. There was never a category of books that was initially accepted and rejected later.
The Gnostic gospels and writings related to them, written after the New Testament books, were called the “pseudepigrapha,” which means false writings. They were called this because the authors utilized the name of some apostle rather than their own name. For example the gospel of Thomas or Peter was added as the author. These books were not written by the apostles but by men writing in the second and later centuries, long after the apostles had died. These writings reflect the beliefs of Gnosticism and not Christianity. Gnosticism teaches that the material world is evil and the spiritual world is good. Salvation is not by grace or works but upon the acquiring of special knowledge (gnosis) of one’s true condition. The “pseudepigrapha” writings contradict the teachings of scripture, which was one of the primary tests of canonicity. These books were rejected by the early church.
 Greg Koukl, “No Lost Books of the Bible,” STR Commentary January, 29, 1994
 Norman Geisler & Ron Brooks, When Skeptics Ask, Baker Books, 1996, p. 153-154