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    I have already zeroed the stage2 file, dd if=/dev/zero of=/boot/grub/stage2 bs=124k count=1. It didn't effect the system at all. Commented Jan 31, 2016 at 13:54
  • please do a sudo grub-install /dev/sda and reboot Commented Jan 31, 2016 at 13:56
  • according to this, it should work en.wikipedia.org/wiki/GNU_GRUB Commented Jan 31, 2016 at 13:59
  • grub-install /dev/sda has regenerated /boot/grub/stage2 binary and system is still bootable. Commented Jan 31, 2016 at 14:02
  • maybe dd is creating a new file actually instead of overwriting the old one. Commented Jan 31, 2016 at 14:02