The city of Bethel was originally called Luz. The location was renamed by the patriarch Jacob (Genesis 12:8, Genesis 28:10 - 19).
The city of Dan was first called Leshem (Joshua 19:47) or Laish (Judges 18:7). It received its new designation after the tribe of Dan slaughtered its inhabitants, repopulated the area with its own people, and renamed it after the tribe's founder (Joshua 19:47).
Debir (Joshua 15:15) was originally referred to as Kirjath-sepher (Joshua 15:15) or Kirjath-sannah (Joshua 15:49).
Engedi, near the Dead Sea, was originally referred to as the city of Hazazon-tamar (Genesis 14:7, 2Chronicles 20:2).
Biblical commentaries speculate the city of Ephraim (John 11:54) may have been originally known as Ophrah (Joshua 18:23) or possibly Ephron (2Chronicles 13:19).
The city of Hebron was first called Kirjatharba (Genesis 23:2, Joshua 14:15) or Arbah (Genesis 35:27). It included an area of oak trees, considered part of the city, named Mamre where Abraham, Isaac and Jacob resided for part of their lives.
The city of Hormah, first called Zephath, received its new name after the tribes of Judah and Simeon conquered it (Judges 1:17).
The capital city of Jerusalem was originally called Jebusi or Jubus (Joshua 18:16, 28, 1Chronicles 11:4). Its name was changed after King David conquered it and made it the new capital of a united Israel (1Chronicles 11).
Zoar's original name was Bela (Genesis 14:2, 8).
Old versus New
The original KJV Old Testament names for the following cities were changed and then recorded in the New Testament.
Accho (Judges 1:31) changed to Ptolemais (Acts 21:7).
Ashdod (Joshua 11:22) changed to Azotus (Acts 8:40).
The city Aphek (Joshua 12:18) had its name changed to Antipatris (Acts 23:31).
The sea of Chinnereth (Numbers 34:11, Joshua 13:27) received three different Biblical designations in the New Testament. They were the sea of Tiberias (John 6:1), Gennesaret (Luke 5:1) and the sea of Galilee (Matthew 4:18).
Chittim (Numbers 24:24) changed to Cyprus (Acts 4:36).
Japho (Joshua 19:46) changed to Joppa (Acts 9:36).
Lod (1Chronicles 8:12) changed to Lydda (Acts 9:32).
The city name Zarephath (1Kings 17:9) changed to Sarepta (Luke 4:26).