2.6 is more difficult as the file paths have changed a bunch. Best thing to do is just start with a fresh image and just reconfigure controls as they are much easier to configure than they were for 2.6.
It’s hard to check a version as retropie is modular and pieced together from so many systems. I honestly just always start with a fresh image, but I don’t play my pi often enough to merit enough customisations that I’d worry about losing anything in an update.
But as long as you’ve updated your setup script before a full binary install and it doesn’t throw any errors you can probably safely assume you’re on the latest version.