Joshua and the Israelites almost totally wiped them out, but some survivors did escape to the fortified cities. ¹ 

When they finished dividing the land into its regions, the Israelites gave Joshua son of Nun some land. ¹ 

If ¹  you abandon the Lord and worship ²  foreign gods, he will turn against you; ³  he will bring disaster on you and destroy you, ⁴  though he once treated you well.” ⁵ 

When Israel had finished killing all the men ¹  of Ai who had chased them toward the desert ²  (they all fell by the sword), ³  all Israel returned to Ai and put the sword to it.

These are the land assignments which Eleazar the priest, Joshua son of Nun, and the Israelite tribal leaders ¹  made by drawing lots in Shiloh before the Lord at the entrance of the tent of meeting. ²  So they finished dividing up the land.