Hi! Did you mean that you can see the duplicated files using ssh but you can’t delete them? If you can see the files, and you are logged in as root, you will be able to delete the files:

:~$ sudo pi@xxx.xxx.xxx.xxx

When connected write:

:~$ sudo passwd

Write the password that you want, exit ssh session and try connecting with:

:~$ sudo root@xxx.xxx.xxx.xxx

You can try deleting files using cmd, but for managing files I recommend FileZilla, it’s easy to set up and free…

If you can’t see the duplicated files, and if you scrapped the roms, try deleting gamelist.xml (make a backup first). If the games showed without this file are listed ok, there is a mistake in the file… I remember that if the directory listed on gamelist.xml was in uppercase like MAME, the games showed were not working. Try changing it to lowercase.