i have the Problem that for example the SNES-Emulator always change the retroarchcustom.cfg. The Point video_threaded change from false to true. So the most of the Emulators Freeze. Please help me.
This is obviously way late, but I had the same problem on a pi4.
I figure I might help someone else with this issue.
I added this line to the end of batocera.conf
It persists even after a reboot.