Over the Air Folder Management happens every 24 hours I believe. However this should have happend automagically.
If you have desktop manager running, one thing you can do is connect the BlackBerry, open desktop manager, open backup and restore and click on advanced. Find the folders and folder id's databases on the right, highlight each and click clear. Disconnect the BlackBerry and reconnect it to rebuild those databases.
Or, if you don't have desktop manager, try filing something in outlook that is also on the handheld. This will kinda force the Over the Air Folder Management to kick in and should recreate the folder structure.