Had this problem with the latest “Stable” version 5.27.2, so I decided to update to the latest beta version through the menus and no longer have the problem with restarting the system after making changes.
Odroid N2+ 4GB
64GB SD card for installation media
64GB EMMC for Rom storage
Housed in an Arcade Fightstick from MicroCenter
Batocera v29 12/03/2020 21:23
Update: Problem is still present, it happen after I tried to shutdown my system, then powered it back on, then went to see if I can still restart and the problem came back.
Update #2 After another power down, it seems to be working fine again. I hope this issues can get fixed, I love my N2+