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Compare Matthew 24:38-40 with Revelation 14:14-20. In Matthew, the unbelievers are taken(vs.39), but in Revelation, the unbelievers are left behind.

This needs an explaination.
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First, the assumption you have here in Matthew that these are unbelievers is not founded in the language the Apostle uses. The same word for taken, is also the word used for when someone receives Christ as their Savior.

Rapture verbs—the general English meanings of the Greek words used:

• MT 24:31 to come upon, come after
• MT 24:40 to take over, to receive, to inherit
• MK 13:27 to come upon, come after
• MK 16:19 to carry up
• LK 9:51 a taking up: ascension
• LK 17:34-35 to take over, to receive, to inherit
• LK 24:51 to take up, raise
• AC 1:9-11 to lift up
• 1CO 15:51-54 to change
• 2CO 4:14 to waken, to raise up
• 2CO 12:2-4 to seize, to catch up, to snatch away
• 1TH 4:16-17 to seize, to catch up, to snatch away
• 2TI 2:18 (resurrection) a standing up, a raising up, rising
• 1TI 3:16 to take up, raise
• HEB 11:5 to transfer, change
• REV 12:5 to seize, to catch up, to snatch away

Now when you get to Revelation, you have to understand how the book by John is constructed. He uses parallel accounts to cover the myriad events. This makes Revelation difficult to read because the general rule of linearity in the Bible is punctuated with overlapping timelines. You cannot read through Revelation like a novel! To look for parallel construction, look for discernable breaks when John changes both scene and focus.

Now the section you have referenced starts in Rev 13:1 and goes through the end of chapter 16. Chapter 13 describes the rise of the Antichrist during the first half week. Notice the call once again for the believers at verse 13:10b: "This calls for patient endurance and faithfulness on the part of the saints." This repeats other admonishments to 'keep the faith,' or "stand firm." (I would advance the idea that a systematic review of 'chosen,' 'elect,' and 'saints' are how the Bible does refer to Christian believers even though we don't like to use those titles for ourselves.)

The change at chapter 14 shows the same type of opposing sides as found in Daniel 9:27 to each half week of the seventieth 'seven.' Like Jesus' Olivet Discourse in the Synoptic Gospels, you have another sequence of events laid out in linear fashion.

• Jesus arriving on Mt Olives returning as He went
• The 144,000
• 3 Angels, the first of which fulfills the Great Commission Jesus said would come before the end in Matthew 24:14
• A proscription praising those “left behind” and martyred for God (at least two – which completes the fifth Seal)
• The Harvest of souls

Now about the Harvest.

First of all, it should be established as an underlying principle that flesh and blood cannot inherit the Kingdom of Heaven (1CO 15:50) but our earthly body will be changed into a spiritual body albeit physical (1CO 15:44). And while most will be raised from the dead and they get to go first (1TH 4:16) some will be caught up that are still alive and are left (1 CO 15:51; 1TH 4:17).

However, does God need our physical earthly bodies? Not in Heaven as from rule one. God doesn’t need them; we are going to be changed after all in a twinkling of an eye (1CO 15:52). And since most of the great Multitude will be raised from the dead, 90-99% of all the souls will not have physical bodies to part with as they been dead so long as to have decayed to nothingness. However, God will raise up the dead imperishable (1CO 15:42). So it follows that He does need to recreate their flesh and blood in order to change it into the spiritual body. The soul goes from Paradise directly into the new spiritual body.

But what about those that are still alive and are left? What happens to their bodies? Well if God can raise those that are physically gone directly into their spiritual bodies as with most of the chosen, does God need our flesh and blood for Him to change it? No. We have just proved that with those asleep in Christ. The change we are to undergo does not have to change flesh and blood into something spiritual, but can also be a direct transference into the spiritual body we will have.

This asks a question about what happens to the flesh and blood we leave behind, because while we know that our bodies can’t inherit the Kingdom of Heaven, we will. This does tend to give us a scenario whereby the events foretold by Christ in the Olivet Discourse and Revelation could be fulfilled. Since we know that some will not die, how is it that Jesus answers where the living will be taken by describing them as dead bodies? Well we have already established that one, some of us will not die, and two He does not need flesh and blood to create a spiritual body, why does He describe in Luke where we will be taken will have dead bodies?

Those that are still alive and are left could leave lifeless bodies behind, because God doesn’t need that part. He will prepare our imperishable and immortal bodies, and all that is required is our soul. Thus, this taking of our souls out of our flesh and blood bodies would not be like experiencing death, and we will all be changed, but we will not all die. In a manner of speaking, Jesus told the disciples where they would physically go, because at that time no one knew where He had come from and where He was going.

Now we have to ask, what happens to our bodies that we no longer need? Well think how this will affect the unbelieving world which will be 99% of those left behind. (Some still are martyred in Christ after the Rapture to complete the fifth Seal.) They have been terrified by a great earthquake, the sun/moon/star event and maybe even a second earthquake with the scrolling of the sky. These people who worship the beast from the greatest to the least are cowering and crying out for the rocks to fall on them and hide them from God. Now in just one day, the harvest comes, and no retribution falls upon them from the terrible God in the sky, but lo and behold, the next day, here are all these lifeless bodies without a mark on them, some in the prime of health.

And the world will realize these are the people they have been persecuting, and that these people who looked to the Lord for Salvation seemingly have been slaughtered by the millions. Think of the fear this would send into the world of the God they’re afraid of but won’t worship. And, this would be the greatest one-time occurrence of death since the Great Flood.

Now one of two things could happen or be done in tandem. God could terrorize them further, and press the bodies and make the blood flow. He’s going to turn all the sea, water and springs to blood before he’s through anyway, so having blood flow this deep for a couple of hundred miles is just a little taste of things to come. In such an occurrence, carrion birds certainly will flock there. It could happen; we have already established he doesn’t need the bodies of flesh and blood. Or the world will have to do something with what will be the world’s greatest sanitation problem. They will have to collect the bodies and dispose of them, in which case you can expect carrion birds to gather around that process too.

At any rate, we as the Church should not be alarmed. I for one, don’t need this old body wracked with ailments and infirmaries and would gladly exchange it for a heavenly body and wouldn’t care less what happens to the discarded model.

Furthermore there is also evidence in the Old Testament about the Rapture. One that succinctly uses the Harvest analogy is contained in Amos: (from the NIV)

AM 8:1 This is what the Sovereign LORD showed me: a basket of ripe fruit. 2 "What do you see, Amos?" he asked.
"A basket of ripe fruit," I answered.
Then the LORD said to me, "The time is ripe for my people Israel; I will spare them no longer.

AM 8:3 "In that day," declares the Sovereign LORD, "the songs in the temple will turn to wailing. Many, many bodies--flung everywhere! Silence!"

If it offends you that God would discard your body, (read John 6:61) think how offensive it will be to the world - and they reject God, so be careful in what you take offense to. However, to put the whole of the Bible into a systematic review there are too many references that point to just this. The conclusion I have reached is that this Harvest is a harvest of souls, because the flesh cannot inherit the Kingdom of God, as Jesus said in John 6:63 that "the flesh counts for nothing."