The Body of Christ or The Church is all Born Again believers by the Spirit who are in Christ Jesus.
The "churches" are a mixture of believers and non-believers and when the non-believers have the greater influence the church becomes sick and eventually dies from lack of The Spirit.
In The Book of Revelation Jesus writes 7 letters to 7 churches. He addresses each church and evaluates their condition and effectiveness.
The only church He approves of without any judgments wit...h warnings is the church of Philadelphia.
All the churches were considered to have some true believers in them - they being a part of The Body of Christ - The true Church.
So what happens to all the churches who's works or relationship is not right with Jesus ?
Keep in mind - we are not talking about buildings, denominations or general assemblies - we are talking about PEOPLE who's works and relationship to Jesus are either approved of or not by God. We are also not talking about salvation but performance here.
Those People who are counted worthy (works and relationship to God - approved) will be raptured as a bride to Christ.
Those who are not approved or worthy - were warned to repent and return to their first love or else - God disciplines those who belong to Him.
All of the other churches who are not of the same mind and Spirit (approved) as the church of Philadelphia will enter The Great Tribulation to separate the wheat from the chaff - believers from non-believers. Because - they were not ready when the groom came for His bride.