According to the medrash pirkei deRebbi Eliezer (48) 200,000 Ephraimites left Egypt many years before Moshe took the Jews out and were killed. There are other midrashim and a gemarah which quote alternative figures, however all of them put the figure well into the tens of thousands if not more. However whenever a census is taken of the Jews in the desert Ephraim's numbers do not seem to be any less than any of the other shevatim. Why doesn't shevet Ephraim's numbers seem to be affected by the large group which left early and was killed?
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Unsourced, but it makes sense to me that the Bnei Efraim chaffed under Egyptian rule after having been princes themselves in Egypt. The fact that they tried to leave early, multiple times according to one pirush on Shemos Rabba 20:11, indicates that. So then I would assume that when 4/5ths of the Jews died during makkat chochesh that the Bnei Efraim were probably much less affected. The Jews that did were those who did not want to leave Egypt. The Bnei Efraim were clearly itching to get out.