As mentioned in the Installation section, all the local user data is saved at ~/Library/Application Support/FontBase or ~/Application Support/FontBase on Mac and C:/Users/USERNAME/AppData/Roaming/FontBase on Windows.
To completely reset the settings and user data, all you have to do is remove this folder (we do recommend making a reserve copy beforehand, in case you change your mind after). Please keep in mind that this will reset the settings, as well as remove all the user-created collections and tags.
This will not affect the fonts or folders you've added into FontBase. Once you've closed FontBase and reset the settings, just re-open the app and it will run as if freshly installed. If you don't see your fonts or folders right away - no worries, most likely you just need to set your Root folder location in the Settings page back to where it was before the reset.