[{"_id":"6245131fdbcda3639d75c951","username":"joy","data":[{"_id":"6245131fdbcda3639d75c953","value_1":"hello1","value_2":"thank you1"},{"_id":"6245131fdbcda3639d75c954","value_1":"hello2","value_2":"thank you2"}]}]

db.collection.update({username:"joy"},[{$set:{data:{$concatArrays:[{$filter:{input:"$data",cond:{$ne:["$$this._id","6245131fdbcda3639d75c953"]}}},[{_id:"6245131fdbcda3639d75c953",value_1:"change data from hello1",value_2:"change data from thank you1"}]]}}}])