The verb in this instance seems to signal the defeating of Ephraim, though not (yet) the killing of the 42,000. Thus, the defeat here is not the end of the story. As Kuruvilla notes, Victory will no longer suffice; to expunge the slight [Ephraim’s taunt], only blood will pass muster. No quarter will be given. The Gileadite onslaught is unstoppable, and the Ephraimite militia is smashed.
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4 Then Jephthah gathered all the men of Gilead and fought with Ephraim. And the men of Gilead struck Ephraim, because they said, “You are fugitives of Ephraim, you Gileadites, in the midst of Ephraim and Manasseh.”