Hi and welcome to Arturia forums.
Perhaps the manual does'nt provide enough information about this.
There are none User presets from the application installer. Your own presets are User Presets.
There are Factory Presets and templates by default, and it should'nt be possible to overwrite them. So are you sure you have overwritten anything? What presets (Specific names) have you written over?
If you somehow have lost presets that came with the application installer, then you can re-install the application, if you have'nt created a back-up of the presets you can copy to the folder where the presets are installed. I suggest you create back-ups of any User Presets before any re-install - just in case.
FYI: The path to the installed, saved and imported presets depend on if you use Windows PC or MAC.
WIN: C:\ProgramData\Arturia\Presets
OSX: /Library/Arturia/Presets
(Keep in mind you also can export preset banks.)
If it's only the User bank attribute you are missing, then you can just add one again. A bank with no presets will vanish untill you add it again containing at least one preset.
I think the empty User bank attribute in the bank section that was originally is taking away by an update if there was none presets in the bank, but it does'nt matter. Actuallly it can help to see you can add your own banks and make your own User bank attributes.
