Those files do not exist until you modify them, as only the changes you make are written to the file, overriding the automatically generated defaults.
If you want to reset to the default menu contents et al, just remove the files. To be on the safe side, move them some other place first:
mv ~/.config/menus/applications.menu ~
mv ~/.config/menus/settings.menu ~
You now have the backup files in your home directory. If for some reason you want to restore the files to their previous state, you can move them back like so:
mv ~/applications.menu ~/.config/menus/
mv ~/settings.menu ~/.config/menus/