If I am understanding your question correctly, you want to make certain changes in RGUI and for them to be permananent?
There are a few ways to go about this, but I find the following way the best in order to keep the RetroPie config in place so that you wont encounter future problems, although I am sure there are other ways.
What I do is
– Run the game, enter RGUI, then select to save my config
– This will write out a (new) config file in the directory of the system you were using.
– I then make my changes in RGUI and save it again, this will create another config file.
– I compare the two for differences (usually only a couple of lines) then I manually put those lines into either the main retroarch.cfg (if I know I want the change for all systems), or I drop the change into the system specific retroarch.cfg
But I’m happy to do that for you – all I need is to know which system you are playing when you set the RGUI settings, e.g. SNES. And then when you save the settings – you will see the filename saved shown in yellow text at the bottom of the screen – I need that file.
I can then tell you a couple of lines to change and it will remember it.