I'm a bit confused - the right permissions for the gamelists are to be owned by the user pi. If you change the file to be owned by root, then Emulationstation (which runs as user pi) will not be able to save any metadata (writing back the gamelist.xml file).
Make sure the files are owned by the user pi, then try again to see if the metadata is saved. If it's not, show a screenshot of the file's permissions. Also, make sure you didn't accidentally disabled saving the metadata on exit from the Emulationstation settings.