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Where did they come from, your “Jews that didn’t flee”?

Egypt. Just as other Jews. You might notice that Islam is quite a bit younger than Judaism (or indeed Christianity). Rough overview:

The tribes flee Egypt follow Moses etc. settle in what's currently Israel. The Babylonians came, saw, and ethnically cleansed Israel, throwing Jewry into diaspora. Persians then stomped the Babylonians and allowed Israelites to return to those areas, that was >500BC. It roughly coincides with Judaism becoming monotheistic. They build a second temple, Persians are thrown out by Greeks, Israelis half-way throw out the Greeks (limited autonomy), Romans kick out the Greek, some upstart Rabbi starts a new religion, gets crucified, about 600 years later a lad named Muhammed founds another religion which lots of people like, among those a lot of people living in Israel. Some also don't like it, and don't convert, just as before with that Jesus guy but Mohammed is a lot more popular. Thus you have Muslim, Jewish, and Christian Palestinians, roughly in that order. Then nearly 1500 years later diaspora Jews come and want to settle there and, because it coincides with the age of nationalism and fascism, a fuckton of mistakes are made -- to wit, the likes of the Stern Gang. The rest is recent history and more recent mistakes, to wit, the pudding prices (SCNR).