I don’t know if your internal changes will let you get things back to muOS defaults at this point, but it is worth trying.
Go to applications>task toolkit>restore tasks and restore retroarch configs.
Open retroarch through the applications menu, populate you retro achievements credentials, get back to main menu, go to configuration file>save current config.
If want to make any other change to retroarch globally, you will need to enable retroarch config freedom.
But the recommended way is to use overrides for the other settings.
There’s nothing more to it.
I use achievements in all of my devices, and it just works.