Remember that reconciliation will not happen instantainously no matter where you delete it from. Email Rec can take up to 15-20 minutes or longer depending on how much the user uses their BB. Essentially it happens on the mialbox rescan, but if the user is always using their bb it takes longer.
If they do a reconcile now and it works then it will work on it's own, it's just a matter of time. There is no setting to change either, it's just how the BES functions.
And the BES doesn't trigger any commands for email rec as well. When you read a message on the BB the BB lets the BES know to update the property of that message on Exchange to read. When you read an email on Exchange the BES will see the property change and update the BB upon scanning the mailbox.
At no point is the BES told to make those changes, it just happens when you force the reconcile or when it rescans the mailbox on it's own. It's all a change in the property of the message and is not a priority.
That's how it's been explained to me and it makes sense. I beleive that instant email rec would drain the battery and place a heavier load on the BES to have to be constantly accessing the mailbox and updaing the BB.
If anybody knows of any mistakes or things to add by all means let me know so I don't make an a$$ out of myself
Maybe it will be instant in the future but I haven't heard anything yet. Hope that helps to clarify the process.