I had the same thought -- the docs say this (Admin Guide, page 80):
Quote:
Managing the wireless backup and restore of organizer data
Automatic wireless backup is designed to back up user account settings and data from the BlackBerry device to the BlackBerry Enterprise Server automatically, without user involvement. Wireless backup on the BlackBerry Enterprise Server enables you to synchronize organizer data to new BlackBerry devices without impacting the performance of the messaging server. See “Appendix: Wireless backup and restore” on page 141 for more information.
If the BlackBerry Enterprise Server is not writing a user’s organizer data from the BlackBerry device to the BlackBerry Configuration Database correctly, the existing backed up organizer data on the BlackBerry Enterprise Server might be corrupt. Delete the organizer data from the BlackBerry Enterprise Server. Deleting the organizer data forces the user’s BlackBerry device to synchronize with the BlackBerry Enterprise Server over the wireless network.
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So everything is recreated by the system. No idea how much impact this would have -- maybe do it a 100 users at time?