MYSQL UPDATE with IN and Subquery

Try:

UPDATE entry
  SET total_comments = (SELECT COUNT(*) 
                        FROM comments
                        WHERE entry.id = comments.eid
                        GROUP BY id)

Use:

UPDATE entry 
   SET total_comments = (SELECT COUNT(*)
                           FROM COMMENTS c
                          WHERE c.eid = id
                       GROUP BY c.eid)
 WHERE id IN ( SELECT eid 
                 FROM comments 
                WHERE id IN (1,2,3,4,5,6))

That's exactly what I'd expect. The id is IN the set you give it, so total_comments = total_comments + 1.

It's not going to add one for each instance of the same value: that's not how IN works. IN will return a simple boolean yes/no.

If you really need total_comments in a separate table, I would make that a VIEW.

CREATE VIEW entry AS 
  SELECT id, COUNT(comments) AS total_comment 
  FROM comments 
  GROUP BY id

This way you avoid the maintenance task of updating the total_comments table altogether.