Try this. At phpmyadmin, run the following query.
Code:
UPDATE `xf_user` SET conversations_unread = 0;
This will take care to turn all the conversations as read so no alerts will be displayed.
2 things to note. First make a thorough backup of the user table before you run the query and if your db tables use a custom prefix then you should use that instead of the xenforo''s default prefix (xf_ ) . Hope it helps.