[{"id":1,"changed":false,"level_2":[{"changed":false},{"changed":false,"level_3":[{"changed":false},{"changed":false,"level_4":[{"changed":false}]}]}]}]

db.collection.update({"id":1},{"$set":{"changed":true,"level_2.$[].changed":true,"level_2.$[levelThree].level_3.$[].changed":true,"level_2.$[levelThree].level_3.$[levelFour].level_4.$[].changed":true}},{arrayFilters:[{"levelThree.level_3":{$exists:true}},{"levelFour.level_4":{$exists:true}}]})