If its just the cowling that has come off and all indications are normal why would you shut an engine down producing thrust. Yes you may have a bit more drag but you'd have an even bigger problem with one engine shut down losing other ancillary systems in the process.
There isn't an SOP that would cover this as this would be an airmanship call. I haven't checked the engine cowl in the Config Deviation List (CDL) which details when you can fly with missing panels etc but I would imagine it would be a Nil Despatch item.