‘ So Joshua smote all the land, the hill country and the South (the Negeb), and the lowland (Shephelah) and the slopes and all their kings. He left none remaining, but he utterly destroyed (devoted) all that breathed as YHWH, the God of Israel, commanded.'
The purpose of Joshua's invasion of the South was to break down resistance and to kill kings and decimate armies, and weaken the cities by destroying all the inhabitants who remained behind so that they would leave Israel alone. It was a softening up operation. In the nature of what he still had to do he could not occupy them or leave men behind in them. It was an exercise in breaking their backs so that later they would be too weak to resist when Israel finally sought to take them over. But many of the people would still have survived, and once Joshua had moved on, would return and seek to re-establish their cities and encampments.
Note the different areas involved, the southern mountains (the hill country), the south (Negeb) which was the semi-desert area on the southern borders with its oases, the low hills (the Shephelah) sloping down towards the plain, the slopes (the meaning of the word is not certain), possibly the slopes and cliffs of the Negeb and the Shephelah. But campaign went on for a long time but he could not cover every inch of ground.