Yep, its not really all that clear at the moment, but in essence, when you save your settings from RGUI it wont save to the retroarch.cfg.
Instead it will write a new config file in the same directory.

You can see it if you type “ls -lah”

Whilst you could simply rename this new file to be retroarch.cfg, that would break a lot of the other links that RetroPie uses.

So the best bet would be to take the relevant lines out of the new file and put them in your retroarch.cfg. I’ll try to cover this in a new video this weekend.