@screech Thanks, but neither is the issue.
There is no gamelist.xml in the Roms/System folder nor in the configs/all....
All are in the /opt/retropie/configs/all/emulationstation/gamelists/system/ folders. Some previous scrapes/xml files from my sega master system are in there. The weird thing is even, when I edit those now the change are not reflected in emulationsstation/gamelist.db. It is as if when scraping/importing xml manually it looks for it somewhere else.
And yes I alsways shutdown emulationstation when changing :)