DISCLAIMER: Repeating these steps may or may not yield the same result.
Ok guys, not sure if this is a fluke or not but decided to throw it out there for people to try and perfect.
I was about to try installing Oneofakindpc's hybrid after being disappointed with the v7 versions, and was about to do a wipe with JLCmdr.
I proceeded like normal putting all of the info the program needs to wipe the phone.
After it connected, (where the screen turns red on the program) i remembered i didnt back up my 3rd party apps since i had reloaded my computer. So i hurried and hit close on the window. My phone then rebooted a few seconds later, and when it came up all of my regular apps were asking permissions just like as if i had got done reloading my backup. This is quite awesome if it turns out to work well, and maybe the makers of jlcmdr can put an option for wiping without wiping apps.
Everything else, however seems to have been wiped liek normal. All settings back to default, no messages contacts etc. Will update with more info once i get the new OS running.
Edit: Also wanted to include that i DID NOT have to reload an OS to get the phone back up and running like normal, so apparantly it does not fully wipe the phone. But could definitely come in handy.