Matthew 17:10-13 is the second occasion Jesus declared John as Elijah. Again, He gives no indication that He expected yet another Elijah to appear. This is Jesus' commentary on Malachi 4:5-6. He is neither indicating there will be another Elijah to come, nor contradicting what He said earlier in Matthew 11. In verse 11, He speaks in a future sense because that is how Malachi 4:5-6 is written. He also did it to emphasize that the scribes had correctly interpreted the prophecy in terms of Elijah preceding the arrival of the Messiah.
Jesus begins the next sentence of His reply with "but," an adversative conjunction indicating disagreement. But means "on the contrary," "conversely," or "however," and it is used here to indicate an exception. Jesus makes it clear He did not agree with the scribes beyond the point that they had correctly taught Elijah must come first. He clarifies further by saying that the scribes did not recognize Elijah when he came and badly mistreated him. Matthew 17:13 clearly establishes that the disciples understood He meant that John was the Elijah of Malachi 4:5-6. In other words, Jesus is saying Malachi 4:5-6 has already occurred—the greatest of the Old Testament prophets already fulfilled it.
What about "restore all things"? Does it refer to doctrine? Not specifically. It is a very general statement. The Greek word means "to put back again," "to reorganize," "to set up," "to bring back," "to reclaim." It can refer to health, authority, or government—or, for that matter, to straightening out or bringing back true conceptions about the Messiah. What did the original Elijah do? He straightened out—restored—right conceptions about who God is because the Israelites had lost sight of Him.
Who says "restore all things?" Jesus does. This is mentioned in no other place in reference to John the Baptist or Elijah. The Bible's marginal references refer us to Luke 1:17 and Malachi 4:6 where nothing is said directly about either Elijah or John restoring all things. Remember, this is Jesus' commentary on what John did. Even as Elijah restored right conceptions about God in his day, John the Baptist restored right conceptions about the Messiah, God with us.
That is not all. John, the Elijah of Malachi 4:5-6, turned the hearts of the fathers to the children and the children to the fathers. Logic demands this refer to his preaching as having a positive impact upon family life. Turning hearts is a fruit, an effect, that happens alongside preparing a people to receive the Messiah.
Malachi 2:14-15 reveals that in Malachi's day the Jewish community was having serious marriage problems. Family problems were extant, and they continued among the Jews down to John's day.
Secondly, this cannot refer to "the Fathers" in terms of Abraham, Isaac, and Jacob because they were dead, and when they died, their thoughts perished. Their hearts cannot turn to the children. What John restored in anticipation of the Messiah's coming were right conceptions about Him, and his preaching of repentance led to right relationships within human families and within the Family of God.
What is lacking in the Bible by God's express design is a detailed review of all John preached. We know only that he was very effective in what he did. We do not know all that he restored, but we can understand that he restored everything necessary for the Messiah to be recognized and received. To take "restore all things" beyond the scope of what was prophesied to be the extent of John's ministry is getting into the area of fanciful interpretations because Jesus confirms both that John was the Elijah to come and that his ministry was great.