Apple has been changing the location of the file which stores your current Energy Saver settings in macOS Sierra, which can cause confusion.
In Sierra 10.12.2, it changed location, from /Library/Preferences/SystemConfiguration/com.apple.PowerManagement.plist (its location in 10.12.1 and earlier) to /Library/Preferences/com.apple.PowerManagement.plist
Now in Sierra 10.12.3, it has changed name. The default settings are now stored in com.apple.PowerManagement.plist (in /Library/Preferences), but your user’s current settings are stored in com.apple.PowerManagement.[UUID].plist, where [UUID] is replaced by your hardware UUID. If you want to check that, it is listed in System Information (About This Mac… and click on System Report…), when you select the top item, Hardware, where it is the last item listed in the main pane.
It is unclear why this change has occurred. I have checked that settings do persist properly after a restart – I was at first concerned that my Mac was going to be set back to its Power Management defaults, but that was not the case.
When you have updated to 10.12.3, particularly if you have a UPS configured in your Energy Saver pane, you may wish to keep a careful eye on its settings, in case UPS-based automatic shutdown is disabled. I suspect that mine was when updating to 10.12.2.