JL_Cmder removes the entire OS from the device, leaving it at a JVM 507 error. The security wipe only removes the data from the device and leaves the OS in tact.
However, you don't need to run either when upgrading your device. I never wipe my device prior to upgrading.
Some people say they do to get a "clean" install, but a wipe is done during the install process prior to loading the new OS. I never ran into any issues doing it this way.
The difference between stupidity and genius is that genius has its limits.
When you take things for granted, the things you are granted, get taken.
Even a mosquito doesn't get a pat on the back until it starts to work.
Too many people miss the silver lining because they're expecting gold.
[BES 5.0.3 / GroupWise 2012 HP2]