Here are the steps I followed to get the 8Bitdo SFC30 and NES30 to work after a reboot:
1. Go to this link and download the configuration which you need:
2. From that configuration you will want to add in your preferred hotkey, exit command, save state, load state, etc. These are not included in the posted CFG files.
3. I ended up taking the contents of that .CFG file with my revisions and then pasted the text into the .CFG file for my SFC30 and NES30 .CFG files that already existed. Make sure to remove the existing text as well.
4. Once text is inserted you will want to make sure to save.
5. Now re-open each file and make sure it saved 🙂
6. Last step I did was to delete the .BAK files for each controller that were already in place. THESE backup files are probably what are causing you grief. I am not sure and have not tested my theory that these .BAK files cause the primary .CFG file to regenerate upon reboot. Someone else may know if that is how it works on bootup.
7. Now reboot and game! Everything should work.