Turns out that RIM has finally coughed up a few simple and more drastic approaches to clearing these indicators most of which I don�t like. There should just be a simple tool that will reset them! RIM provides six options that you should go through serially until the message indicator goes away. Truthfully I hate wiping my device just to get rid of an indicator.
From the Knowledge Base:
NOTE: Backup the BlackBerry before performing any database deletion.
Hard Reset the BlackBerry � Pull out the battery
Go to Messages icon and highlight the most recent date, hit the Menu key and choose mark prior opened.
Go to Messages icon and highlight the most recent date, hit the Menu key and choose delete prior.
Change the theme
Delete the Message Database then hard reset the BlackBerry
Wipe the handheld
