You can do this in phpmyadmin, visit the post table (my test post table is called tb_post) then click "SQL" at the top, clear everything in it and paste this
PHP Code:
UPDATE `tb_post` SET `title` = '' WHERE `title` LIKE 'Re:%'
(change tb_post to the name of your post table) and then click go!
Now all posts that have quoted the thread title (they are quoted as Re: xxxnnnxxx) will have been replaced by an empty string.