When you say upgrade as in from 2.6 to 3.0? You’re best off starting with a fresh sd image. Too much has changed for an update to be seamless (always important to make backups before any update)

but if you’re just looking to fix your es_systems.cfg see:

http://pastebin.com/yCT4H8KB

typically there will be a backup es_systems.cfg in /etc/emulationstation

The folders that used to be used have been consolidated. you can see the wiki for the current folder structure: https://github.com/RetroPie/RetroPie-Setup/wiki