Restoring wpa_supplicant.conf [root]
In my case it was necessary to change the owner and group of the file to wifi:

mount -o rw,remount /system
chown wifi:wifi /data/misc/wifi/wpa_supplicant.conf
ls -la /data/misc/wifi/wpa_supplicant.conf
-rw-rw---- wifi     wifi         2343 2016-07-11 10:31 wpa_supplicant.conf


Note: you need a rooted device to do that.