I highly recommend to everyone to read Joseph Wheless classic from 1926, "Is it God's Word?" You can download it for free because it's out of copyright, and read it on Microsoft Reader.
Here's an excerpt from Chapter vii
But the Jebusites continued to inhabit "Jebus, which is Jerusalem" (Judges xix, 10), until, at least, the time when part of the city was taken by David; …
And the children of Israel dwelt among the Canaanites, Hittites, and Amolites, and Petizzites and Hizites, and Jebusites [precisely the nations who were so annihilated that "not a man was left of them to breathe"]: And they took their daughters to be their wives, and gave their daughters to their sons, and served their gods" (Judges iii, 1-6)!
It is a number of times expressly declared: "Nevertheless, the children of Israel drave not out" the very several peoples named, "but they dwell among the Israelites unto this day" (e.g., Josh. xiii, 13; xv, 63; xvi, 10; xvii, 12, 13). Even under the judges they "could not drive out the inhabitants of the valley, because they had chariots of iron" (Judges i, 19).
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… This admission that the children of Israel "dwelt among" the seven nations proves that the 600,000 soldiers of Yahveh had not exterminated the 20-odd millions of inhabitants of Canaan, but remained a small and, as is now to be seen, conquered minority among their vengeful enemies.
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For these several nations quickly took their turn in conquering and subjecting Israel. First, the King of Mesopotamia kept them in subjection for 8 years (Judges iii 8); then the Moabites for 18 years (iii, 14); then the oft-destroyed Canaanites enslaved them for 20 years (iv, 3); then the Philistines for 18 years (x, 8) ; and again for 40 years (xiii, 1); and so on all but continuously until the time of David, though Yahveh had promised: "Ye shall reign over many nations, but they shall not reign over you" (Deut. xv, 6).
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The sacred record contains many instances, of which but a sample or two will be cited here, of the desperate straits to which Yahveh's heroes of the "conquest" were reduced by their exterminated enemies. In the days of Samuel the judge, the Philistines beat the Chosen so badly that the latter sought recourse to miracle or magic, and brought up the wonder-working Ark of the Covenant of Yahveh out of Shiloh, so that, they said, "when it cometh among us, it may save us out of the hand of our enemies" (1 Sam. iv, 3). It is recorded that the Philistines were afraid when they beard of the advent of the Ark, and said: "Woe unto us, for Gods [Elohim] are come into the camp." Nevertheless, they attacked the soldiers of Yahveh at Ebenezer (which was not then in existence; vii, 12), killed 30,000 of them, and, to their own great misfortune, captured the Ark, which they kept until, to get well rid of it, they sent it back to the Chosen accompanied by suggestive golden images of emerods and mice.