Why did Yoshiyah remove the Bamos in the cities of Shomron? The Kusim were living there?
Rashi (from Megilah 14b): Yoshiyah ruled over all of Yisrael, i.e. [also] those of the 10 tribes that Yirmeyah returned.
Radak: The Bamos remained. Also, there were a small number of Yisraelim scattered there, and they still served idolatry - "va'Yizbach Es Kol Kohanei ha'Bamos Asher Sham" (verse 20). Also in Divrei ha'Yamim II, 34:9 it says that there was a remnant of Efrayim and Menasheh in the days of Yoshiyah. Also in the days of Chizkiyah there was a remnant from Zevulun, Asher, Shimon 1 , Efrayim and Menasheh.
Shimon inherited amidst Yehudah, which was not exiled yet! Radak teaches that a remnant remained among Bnei Shimon who dwelled amidst other Shevatim (refer to Melachim I, 11:31:1:1-2 and the note there). (PF)