Just out of curiosity, which es_systems.cfg do you edit?

I always copy the original to /opt/retropie/configs/all/emulationstation and edit it there where it won't get reverted when running updates. Only thing is it also has to be manually updated/synced if additional systems are added as they won't show on the system list if not listed in the customized es_systems.cfg (I'll normally copy-paste from the original file to the copy once the new system is installed). It just saves some of the headache for the future if you have a custom system order you like and don't want to redo it after updating.