Does it uninstall non-existent ones too.

I don't think so, but that's not a problem to do it manually.

Actually, the cool thing is it actually does. I did some reading on it after I posted, should have done that before I posted but I got ahead of myself.
Basically it scans for whatever bsa's are in the folder. It has a temporary database that tracks what has been uninstalled and installed in the INI file. It uses
that for a comparison. So if it finds a BSA in the ini file that isn't in the data files folder, it tries to unregister it, if it finds one in the Data Files folder that isn't
in the ini file, it tries to add it. It was pretty cool, so I wanted to share that.