Ok, I seem to have figured this out by installing WinSCP, navigating to the files listed in the error messages, deleting them, and then running the scraper to regenerate the files. Now to sort out the bluetooth issue....
@amishgamer Yeah, I forgot to use Clone Spy for automatic removal. Found out about that two days ago. Also, there are a few more differently named duplicates that I'm slowly removing for a full release.
I'm currently working on my ideal ROM set of USA>World/Europe>Japan, but I suppose I can fix up those batch files in the meantime.
@dcm91 I really don't know where the gamelist.xml will be placed because I have no idea how this image is set up. These files can go in 2 places, within each system ROM folder or in /home/pi/.emulationstation/gamelists/systemname. Or at least that's where they go in the standard image. They could be absolutely anywhere on a custom image. You'll just have to try it and see.
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 :)