[{Source:{Code:"Code",Description:{"en":"test","fr":"testfr","def":"test"},_id:"SomeID"}},{Source:{Code:"Code",Description:null,_id:"SomeID"}},{Source:null},{OtherField:1}]

db.collection.aggregate([{$project:{Source:{$arrayToObject:{$filter:{input:{$objectToArray:"$Source"},cond:{$ne:["$$this.v",null]}}}}}},{$addFields:{"Source.Description":"$Source.Description.en"}},{$project:{Source:{$cond:[{$eq:["$Source",{}]},"$$REMOVE","$Source"]}}}])