query optimization for update nested query IN(SELECT
How about:

UPDATE 
(select * from TABLE_NOTE
where COL_NOTE_BIBID = $projectID
join TABLE_PINENOTEREL on $COL_PILENOTEREL_NOTE_ID = $COL_NOTE_ID
WHERE $COL_PILENOTEREL_PILE_ID = $pileId)
SET COL_NOTE_DISPLAY='BLOCK'