There is The Church or Body of Christ but, then there are the churches (believers) that Jesus sent letters to. Not all the "churches" at the end of the church age are raptured. The only church raptured is the church of Philadelphia. All the rest of the churches must listen to what the Spirit is saying to them to repent and change.... "churches" or be cast into Great Tribulation.
 
The Church is not in Heaven.........The bride is... and all who will listen now.

The Spirit and the bride (now) say, “Come.” And let the one who hears say, “Come.” And let the one who... "is thirsty" Come; let "the one" who... "desires", take the water of life without cost. (without cost now - later in Great Tribulation it will cost you)