I know this sounds like an odd solution but when in emulationstation in the quit menu select quit emulationstation- not shutdown or restart. Then it should write the changes. Then go back into emulationstation by typing emulationstation in the terminal or reboot and see if the changes stick.
Test it with only a few first just to make sure it works first so you aren’t redoing your work.
Thanks for the info, I will try it myself when I get home..
But what about changing “sort by” option? It doesn’t seem to remember what I choose..
I’m guessing that it’s a perission problem, and I wonder how to fix it?