This is a fairly straightforward question and the answer is already given with the writings of John:
The Gospel of John does not explicitly predict a grand, future corporate apostasy of the Christian Church in the way Paul does in 2 Thessalonians or Timothy, but it does record Jesus warning about individual defection, betrayal, and false disciples (such as Judas Iscariot or disciples turning away in John 6:66).
The letters of John however state the same danger as Paul. In John’s letter the beginnings of the apostacy are already here: In 1 John 2:18, the Apostle John writes that it is the “last hour” and notes that “many antichrists have come,” showing that the break from true doctrine was a current reality. John speaks of those falling away but remaining nominally Christian as that those who left the community: “They went out from us, but they did not really belong to us,” since they have manifested an active departure from the foundational teachings of Christ. John warns there and now of false teachers who already denied that Jesus Christ had come in the flesh (1 John 4:2–3, 2 John 7)
So unfortunately John 16:13 only describes what it describes, that the apostles and those who stayed with their teaching were guided into all truth. And the composition and compiling of the New Testament is a product of that guidance into all truth.
But immediately, even in Acts we see examples of falling away, and this gathers pace in the letters, until by the end of the New Testament both Paul’s letters and also the letters to the Seven Churches in Revelation, are clearly indicating that the corrupt Christianity will quickly outnumber the true Christianity – and worse still, that the corrupt church will persecute the true church. As happened.
However, this does not mean that the minority is always right. If someone finds themselves completely isolated that is not the same as saying that “a few” will remain faithful. If it is one person who thinks that even the faithful minority are wrong and he or she is the only one who is right then there are lessons to be found in Matthew 18 where Jesus teaches resolving such a situation by bringing the dispute of individuals to the church.
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