MySQL 8.0

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select version();

version()

8.0.36

create table users(id int, group_in json);
insert into users values (1,"[1,2,3]");
insert into users values (2, "[1,3]");
update users set group_in = (select new_grp from (
select id,json_arrayagg(grp) new_grp from users, JSON_TABLE(group_in, "$[*]" COLUMNS(grp INT PATH '$')) as grp_id
where id=1 and grp<>1 group by id
)X
)
where id=1;

Rows matched: 1  Changed: 1  Warnings: 0

select id, json_extract(group_in,'$[*]') from users;

id
json_extract(group_in,'$[*]')

1
[2, 3]

2
[1, 3]