I am having the same behavior with my SFC30 Controller. Last night I too had it working until I rebooted. The configuration was replaced with the .BAK file within same folder. At first I thought I did not save the changes to the mappings when I first edited the joystick file for the SFC30 but after a second reboot, the mappings were all messed up again.
A few thoughts I had for testing tonight
1. Delete .BAK file once the joystick file is set perfectly
2. If that does not work, locking the file so it cannot be altered
I will report back what I find out. I see others are having lots of issues with the 8Bitdo controllers as well.