Hello, Levantine archaeology masters student here.

The answer is that there is essentially no evidence for the total destruction of Levantine peoples associated with the rise of the territorial kingdoms of Israel and Judah. In fact, many archaeological sites in the region are characterized by continuity from the Iron Age I (generally before these kingdoms) to the Iron Age II when they existed. Within the biblical narrative, these conquest stories relate to the idea of the children of Israel coming from outside the region (such as from Egypt in the books of the Torah) and conquering the land. In the archaeological record, we see a different story where Israelite and Judahite material culture is related to local Canaanite culture before it. The presence of Israelite rule over sites like Megiddo is itself hard to archaeologically identify or date and debates about the exact timing and strata of the territorial expansion of these states persist. That there was a people called Israel in the southern Levant in the Late Bronze Age is even evidenced by a victory stele of the Egyptian pharaoh Merneptah, son of the more famous Ramesses II, which claims to have wiped them out, the hieroglyphic determinative for Israel signifying a seemingly tribal people.

There might be biblical textual specialists who can talk about this better but the Book of Deuteronomy is a fairly late work among the Torah, generally seen as having been written by members of the Levite priestly class of Judah written either in the reign of Josiah (641-609 BC) or later in the Babylonian exile or even the Persian period. Its treatment of early history is largely retrospective and comes from the perspective that the Israelites and Judahites had become the rulers of their lands at some point which they knew had been ruled by others before. It’s hard to get in the minds of biblical authors that deep but they may have had the perspective that some violent action must have occurred to explain this change.