Merneptah continued the campaign into Canaan, to destroy the power-base of the coalition. In the long list of his exploits, it was said that "Israel's seed is no more". The hieroglyphics show Israel as a personal name, suffixed by the symbol for a group of people, as in "Israel's clan" (i.e., Jacob's descendants). Scholars have always assumed that this meant the destruction of Israel in Israel (i.e., in Canaan). But we also have Israelites in the delta, and some of them sided with the Sea Peoples against the pharaoh. So the epitaph might have meant that Merneptah went after Israelites wherever he could find them. Obviously he missed a few, since the Israelites persisted underground, and re-emerged later. But for the time being, they were suppressed.
Shortly thereafter, Merneptah abandoned Pi-Ramses, thus eliminating all of the jobs that had been provided by the public works projects. All of those from Canaan were then "free" to return home. As descendants of Abraham & Sarah, who had been granted the land by Amenhotep III, these delta dwellers returned to Canaan to claim their inheritance. From this "Exodus" we get the stories of the Israelites leaving Goshen and being pursued across the desert by the pharaoh. Once again, it's possible that a pharaoh released people from bondage, publicly showing magnanimity, only to attempt to slaughter them in the wilderness. So they weren't just freed — they were freed with a vengeance.1
The brutal conquest of Canaan described in the Book of Joshua actually isn't such a good fit for Joshua's exploits in , which were far more limited in scope, and which didn't involve any sort of systematic eradication of Canaanites. Rather, the details are a much closer fit to Merneptah's campaign in the Levant. But this too became part of the story of the Israelites, who had been freed from bondage in Egypt (after joining the Sea Peoples alliance and losing), thereafter fighting a few battles that the pharaoh wanted to occur in the wilderness, and then claiming their inheritance in Canaan, at the expense of whoever was currently there. Since Merneptah's exploits were written directly into the Torah, it's possible that the Israelites were camp followers, or even an advance force of mercenaries who had been promised land in Canaan as the spoils of war. And even if that was a small number of people, all of the people who intended to persist in Canaan after Merneptah's triumph would have claimed to have been in that group, whether they were or not. And so it was written.