SELECT id
  FROM analyzes
 WHERE code IN
       (SELECT code
          FROM analyzes
         WHERE deleted = 1
         GROUP BY code
        HAVING count(code)>1)

SELECT code, deleted, MAX(deleted_date) FROM analyzes WHERE deleted = 1 GROUP BY code, deleted;

SELECT id, code
FROM   analyzes t
WHERE  deleted = 1
AND    deleted_date =
       (select max(deleted_date)
        from   analyzes a
        where  t.code = a.code
        and    a.deleted = 1)

create table `analyzes`
(
  `id` int,
  `code` varchar(10),
  `deleted` int,
  `deleted_date` int
);

insert into `analyzes` (`id`,`code`,`deleted`,`deleted_date`) values
( 1,'01.00.002',1,1),
( 2,'01.00.002',1,2),
(15,'01.00.002',1,3),
( 3,'01.00.005',1,2),
(17,'01.00.005',1,1),
(16,'01.00.006',0,1),
(18,'01.00.007',1,1),
(19,'01.00.007',0,2);

select * from `analyzes`;

with `t1` as (
  with `t0` as (
    select
      `id`,
      `code`,
      `deleted_date` ,
      max(`deleted_date`) over(partition by `code` order by `code`) `deleted_date_max`
    from `analyzes`
    where
      `deleted` = 1
  )
  select
    `id`,
    `code`,
    `deleted_date`
  from `t0`
  where `deleted_date` = `deleted_date_max`
),
`t2` as (
  select
    `code`
  from `analyzes`
  where `deleted` = 0
)
select
  `t1`.`id`
from `t1`
  left join `t2` on `t1`.`code` = `t2`.`code`
where
  `t2`. `code` is null

with `t1` as (
  with `t0` as (
    select
      `id`,
      `code`,
      `deleted_date` ,
      max(`deleted_date`) over(partition by `code` order by `code`) `deleted_date_max`
    from `analyzes`
    where
      `deleted` = 1
  )
  select
    `id`,
    `code`,
    `deleted_date`
  from `t0`
  where `deleted_date` = `deleted_date_max`
),
`t2` as (
  select
    `code`
  from `analyzes`
  where `deleted` = 0
)
select
  `t1`.`id`
from `t1`
  left join `t2` on `t1`.`code` = `t2`.`code`
where
  `t2`. `code` is null