i found this info in Blackberryforums.com
Need to wipe your device using javaloader or JL_Cmder but don’t want to lose all your 3rd party apps? Backup/Restore in Desktop Manager won’t do it. Here is a way to back them up and restore them. Note: It wouldn’t be a bad idea to do this on a routine basis just incase your device gives you the unexpected hourglass screen of death requiring you to wipe the device.
* Download and install the latest version of Desktop Manager 4.2 from here
* Plug in the device and run Desktop Manager.
* Click on “Switch Device Wizard.”
* Click on “Switch Blackberry Devices.”
* Click “Next.”
* Select USB: Your Pin.
* Click “Next” and then enter your password if required.
* Uncheck “User Data and Settings” and “Include Messages” leaving only “Third Party Applications checked.
* Click “Next.”
* When it’s finished backing up the apps, DO NOT click “Next” or “Cancel.” Leave that screen as it is and continue these instructions.
* Search your computer files/folders for a folder labled with your pin number. Be sure and search in hidden and system files. Hint from BBF member NextelUser: Open Windows Explorer or My Computer and type in %temp% to find your temp folder with the folder labeled as your pin number.
* When you find it copy it to another location.
* Now go back and “Cancel” the Switch Device Wizard. If you cancel the wizard before copying the folder to another location the folder is automatically emptied.
* Now wipe your device as desired. Your backup is complete.
* When the OS has been loaded back to the device run Application Loader again and click on “Add”
* Browse to the folder you copied with your PIN. Double click on the file named yourpin.alx.
* This should add all your 3rd party apps to the apploader.
* Finish the installation to load them to your BB.
* After the 3rd party backups have been restored, move, rename or delete the folder you pointed to using the “Add” feature in DM. Failure to do so will cause subsequent backups to skip any application that was contained in the original backup. See the note below.
* Restore your personal data using the restore feature in Desktop Manager Backup/Restore
Note: If you are wiping the device because of a problem this procedure may not be wise to perform because the cause of the trouble could possibly be in one of the 3rd party apps.
Note: If you ever use one of these backups to restore an app or multiple apps back to your device you’ll need to move the folder to a new location after restoring. If you leave it in the same location then the next time you perform this backup procedure any apps included in the original will not be backed up in the temp/yourpin folder since they are already recognized by Desktop Manager as being in another location. So, after restoring your app(s) simply move the pin folder to a new location, rename it or delete it.