Resetting the system parameters does not change your presets at all. It resets all the system settings you have selected in the setup menu (General, I/O, MIDI/Remote, FC Config, etc.).
Whenever you select a different amp model, it is loaded with all the default settings except for a few key parameters like gain, treble, middle, bass, master volume, etc. All the "advanced" parameters are reset. There's no way to mess up the defaults for amp models.
If you want the factory presets back like they were, you'll need to download them from the Fractal website and reload them.