JL_CMDER is based on javaloader.exe which is made by RIM.
Javaloader 5.0 beta 3 has the following command for wipe:
Wipes the handheld
-a Wipe applications only
-f Wipe filesystem only
The older version of javaloader, which JL_CMDER is based off may not have these options. It sounds like JL_CMDER is performing the following command:
Oh...and another thing...the Bold 9000 has an internal flash memory of 1gB that is separate from the RAM where the OS filesystem is located.