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You can use FileZilla to connect to it and modify the files using that.

On your Raspberry Pi, press F4 to go to the console and type ifconfig (make sure you’re connected to via ethernet or have a WiFi dongle set up). Look for the 4 number address ( or similiar)

In FileZilla:
Host: sftp://the address
Username: pi
Password: raspberry
Port: 22

Click Quickconnect and accept the pop-up thing

Find the file you want to re-write and drag it onto your desktop, modify it and drag it back and replace the older one.

I would also recommend you keep the retroarch.cfg file and company so you can just drag them back in if something goes south (which tends to happen a lot if you mess around in with the configuration a lot or don’t shut down properly).

Have fun! :)