Make a backup of your Data using Desktop Manager-Backup/Restore.
Then use JL_Cmder (in my sig) to wipe the BB. Make sure you've installed the OS to the PC and deleted the vendor.xml (remember, anytime you reinstall the OS package to the PC, or install a new OS package, you need to delete the vendor.xml again. Then connect the BB and run Desktop Manager. Go to "connections" at the top and select USB. Then run Application Loader and it will reload the OS to the BB. See this
thread for more info. When you're done restore the backup you made above.