Her er C#-versionen af det, du har brug for:
var filter = Builders<Item>.Filter.Eq("Id", "a");
var update = Builders<Item>.Update.Set("Array1.$[i].Array2.$[j].Array3", new[] { new Item { Id = "d" } });
var arrayFilters = new List<ArrayFilterDefinition> { new JsonArrayFilterDefinition<Item>("{'i.Id': 'b'}"), new JsonArrayFilterDefinition<Item>("{'j.Id': 'c'}") };
var updateOptions = new UpdateOptions { ArrayFilters = arrayFilters };
collection.UpdateOne(filter, update, updateOptions);