When I first started using a BlackBerry with BES service, everything synched perfectly except for when I deleted items from either Outlook or the BlackBerry.  Here's some information that will help you if you run into a similar problem.

If you delete an email item on  your BlackBerry, and it doesn't delete from Outlook, the first thing you should check is the following setting on your BlackBerry device:

1.  Go into Messages (Email)
2.  Click your Blackberry button (or thumbwheel on older models) and select Options
3.  Select Email Reconciliation
4.  Change the "Delete On" option to "Mailbox & Handheld"
5.  Verify that the "Wireless Reconcile" option is "On"
6.  Verify that the "On Conflicts" option is "Mailbox Wins"
7.  Save your settings

If, on the other hand, you delete an email from Outlook and it doesn't delete on your BlackBerry, the first thing you should think about is whether your Deleted Items folder is emptied on a regular basis.  Your BlackBerry device will only know to delete an email from itself if the email is in your Deleted Items folder in Outlook.  If you empty your deleted items folder (as I used to do, many times a day in an insane bid to keep my mailbox "clean"), any messages emptied that are still on your BlackBerry will remain on your BlackBerry.

So, before you empty your Deleted Items, make sure your BlackBerry is up-to-date (as far as deleted items are concerned).  I don't think the email reconciliation for deleted items is as "real-time" as it for receiving new emails.  I've found the "Reconcile Now" option to be useful in getting emails deleted from my BlackBerry that are in my Deleted Items in Outlook.

If neither of these two things solved your issue, you can request that your service books be resent to your device.

If that doesn't resolve your issue, you may need to do a factory reset on your BlackBerry and do a brand new setup to try to resolve the issue.

(This article gratefully borrowed from: http://blogs.lanlogic.net/)