You have to have emulationstation shutdown to overwrite or place new gamelists files. If you dont the original file simply comes back.
You can use ideelibre solution above or another way is to use a program called Putty on your PC/Laptop.
Get the IP address from your Batocera set up. Enter this into Putty to login. The login = root the password = linux
Once you are logged in eneter the command line /etc/init.d/S31emulationstation stop
You can now go into the roms folders through share and replace gamelists or use scraper software. One you are all done go back to Putty and eneter the command line /etc/init.d/S31emulationstation start
Hope this helps