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    Have you zeroed out the existing file? Because deleting it is unlikely to remove the actual data that grub is referring to from the disc. Commented Jan 31, 2016 at 13:03
  • Took the system back to original state. dd if=/dev/zero of=/boot/grub/stage2 bs=124k count=1. Verified that whole file had been zeroed. Rebooted. System still boots successfully. Commented Jan 31, 2016 at 13:14
  • Comments are not for extended discussion; this conversation has been moved to chat. Commented Feb 2, 2016 at 10:58