[{"_id":1,"depots":[{"_id":1,"isFavourite":true},{"_id":2,"isFavourite":false},{"_id":3,"isFavourite":true},{"_id":4,"isFavourite":false}]},{"_id":2}]

db.collection.update({_id:1},[{"$set":{"depots.isFavourite":false}},{"$set":{"depots.2.isFavourite":true}}])