This was a problem on the Dolphin emulator but the solution may work on all your config folders and is very simple
I poster elsewhere but here is the solution…
"I discovered this very quick and easy solution this morning.
Just go into the Emulators folder where your version of Dolphin is contained, Inside the Dolphin folder go to User and then right click the Config folder where you keep your controller profile (remember to make sure your preferred profiles to use are in the folder before you do this)
After right clicking Config folder click Properties.
Then look at Attributes on the Properties Box and click READ ONLY (ONLY APPLIES TO THIS FOLDER) until you see a tick.
Click apply and then OK then run Batocera/Emulation Station and suddenly it remembers all your controller configs and wont forget it, even if you reload Batocera. It works time and time again,
A very simple solution.
Have fun, Gamecubers,"
