There are no “lost books” of the Bible, or books that were taken out of the Bible, or books missing from the Bible. Every book that God intended and inspired to be in the Bible is in the Bible. There are many legends and rumors of lost books, but there is no truth whatsoever to these stories. There are literally hundreds of religious books that were written in the same time period as the books of the Bible. Some of these books contain true accounts of things that actually occurred (1 Maccabees, for example). Some contain good spiritual teaching (the Wisdom of Solomon, for example). However, these books are not inspired by God. If we read any of these books, the Apocrypha as an example, we have to treat them as fallible historical books, not as the inspired, inerrant Word of God (2 Timothy 3:16-17).
The gospel of Thomas, for example, was a forgery written in the 3rd or 4th century A.D., claiming to have been written by the apostle Thomas. It was not written by Thomas. The early church fathers almost universally rejected the gospel of Thomas as heretical. It contains many false and heretical things that Jesus supposedly said and did. None of it (or at best very little of it) is true. The epistle of Barnabas was not written by the biblical Barnabas, but by an imposter. The same can be said of the gospel of Philip, the apocalypse of Peter, etc.
There is one God. The Bible has one Creator. It is one book. It has one plan of grace, recorded from initiation, through execution, to consummation. From predestination to glorification, the Bible is the story of God redeeming His chosen people for the praise of His glory. As God’s redemptive purposes and plan unfold in Scripture, the recurring themes constantly emphasized are the character of God, the judgment for sin and disobedience, the blessing for faith and obedience, the Lord Savior and sacrifice for sin, and the coming kingdom and glory. It is God’s intention that we know and understand these five themes because our lives and eternal destinies depend upon them. It is therefore unthinkable that God would allow some of this vital information to be “lost” in any way. The Bible is complete, in order that we who read and understand it might also be “complete, and equipped for every good work” (2 Timothy 3:16-17).