In my opinion there would be no clunking if the splines were in good condition regardless of the axle nut torque.
I expect the permanent solution to be "The only remedy would be to replace the axle/shaft and inspect the wheel hub/bearing for similar spline damage which would most likely also need replacement".
https://www.rockauto.com/en/catalog/ford,2017,edge,2.7l+v6+turbocharged,3434543,drivetrain,cv+axle,2288
https://www.rockauto.com/en/catalog/ford,2017,edge,2.7l+v6+turbocharged,3434543,brake+&+wheel+hub,wheel+bearing+&+hub,1636
As far as warranty goes, you would need to loosen the nuts again for them to witness the fault condition and hope that they don't mask the issue but merely torquing the nuts.