Originally Posted by x14
Note: The "Wipe Handheld" function will securely wipe all data from the BlackBerry but will not remove any third party software that might of been installed.
You can use the DM's Backup/Restore function to backup and restore as you need to.
Actually you are given the option to wipe 3rd party software or keep it. I recall being able to choose what to wipe and what to keep.