You could just create a splinter warband. Or rename a recently turned traitor chapter. That happens all the time. 

And the second and 11th legions didn;t go missing. It is implied heavily that they were destroyed by Imperial order. The other primarchs met those others and refused to talk about them for some shameful reason. GW hints that the space wolves destroyed one and the other is actually believed to have been integrated into the ultramarines which accounted in part for their massive size during the crusade.