For a default (non-portable) installation, settings are stored in a combination of the Registry (under
HKEY_CURRENT_USER\Software\Echo Software\PN2) and the User Settings folder. This folder contains Scheme configuration files, caches for scheme and text clip configuration, search terms and other user options. You can find your user settings folder here:
You can delete everything from this folder and PN will continue to function, you will just lose any scheme and clip customizations.