Do you remember exactly what you did to delete the messages via mysql query (and how did you reset the unread count?).
It looks to me as if the total and unread pm counters get recalculated after some functions (the messages are actually counted, not just inc or dec the counters). So while I don't see any specific "fix pm counters" admin function, it looks like if a user does "mark all read" or "delete" from the pm page the counters should be fixed.
If you really wanted to you could probably write a script to fix everyone's counters using the code from build_pm_counters() in private.php.
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