The DELETE_MEMBERS procedure is what are you looking for. To find out more about it please check the official Oracle documentation.
You can do something like:
APEX_COLLECTION.DELETE_MEMBERS
(
p_collection_name => 'collection_name',
p_attr_number => 3,
p_attr_value => '31'
);
Or use the sequence ID.
DECLARE
CURSOR c_temp IS
SELECT
seq_id
FROM APEX_COLLECTIONS
WHERE collection_name = 'collection_name'
AND c003 = '31';
BEGIN
FOR r_temp IN c_temp LOOP
apex_collection.delete_member
(
p_collection_name => 'collection_name',
p_seq => r_temp.seq_id
);
END LOOP;
END;