[{"_id":1234,"outerDucumentName":"someName","nestedList":[{"nestedId":2222,"nestedNestedList":[{"nestedNestedId":3333,"nestedType":1},{"nestedNestedId":4444,"nestedType":2}]}]},{"_id":4567,"outerDucumentName":"someOtherName","nestedList":[{"nestedId":5555,"nestedNestedList":[{"nestedNestedId":6666,"nestedType":1},{"nestedNestedId":7777,"nestedType":2}]}]}]

db.collection.aggregate([{$set:{nestedList:{$map:{input:"$nestedList",as:"ns",in:{$mergeObjects:["$$ns",{nestedNestedList:{$filter:{input:"$$ns.nestedNestedList",cond:{$ne:["$$this.nestedType",2]}}}}]}}}}}])