create table test.tmp_is_primary_phone ( id integer unsigned );
insert into test.tmp_is_primary_phone select min(id) from civicrm_phone where is_primary = 1 group by contact_id ;
update civicrm_phone set is_primary = 0 where id not in ( select id from test.tmp_is_primary_phone ) ;
drop table test.tmp_is_primary_phone ;

-- or ... but this doesn't work (yet)

UPDATE civicrm_email SET is_primary=0 WHERE id NOT IN ( SELECT MIN(id) FROM civicrm_email WHERE is_primary=1 GROUP BY contact_id ) ;