cursor.execute('SELECT * from user where user_id = %(some_id)d', {'some_id': 1234})
records = cursor.fetchall()

insert into phones 
    with t as (select 
        ph.id,
        unnest(ph.phones) as phone  
    FROM 
        phones ph )
    select 
        id,
        array_agg(phone) as phones 
    from 
        t 
    where phone like '%2%' // << место с фильтрацией "неверных" номеров
    group by 
        id 
on conflict(id) do update set phones = excluded.phones