Database
[{"_id":12345,"name":"harold","basicData":{"devices":[{"id":7654,"relatedJson":{"make":"sony","equipmentID":"asdf"}},{"id":9493}],"car":"toyota"}}]
Query
db.collection.update({},[{$set:{"basicData.devices":{$map:{input:"$basicData.devices",in:{$mergeObjects:["$$this",{$cond:[{$ne:["$$this.relatedJson",undefined]},{relatedJson:{$mergeObjects:["$$this.relatedJson",{equipmentId:"$$this.relatedJson.equipmentID"}]}},{}]}]}}}}},{$unset:"basicData.devices.relatedJson.equipmentID"}])