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So back when I used WUBI before settling on using a VM, GRUB was installed (but I messed it up and had to reinstall everything (luckily I backed up)). That was back when I used Vista which starts at LBA 63. Since then, I have switched to Se7en which starts at LBA 2048. I have examined the MBR partition table and determined that on both of them.

Also, I have BOOTMGR on sector 63 on the Vista original disk, but my new disk I recently got has BOOTMGR on 2048. So my question is can I wipe this area of the disk with nulls? Yes I understand that it has to chance to go horribly wrong, but I have an OCD on this (GET OVER IT) and seeing the nulls on drive 2 has made it worse.

Here is the MBR of the disks. The second one isn't a boot drive

HDD1: 00 01 01 00 12 FE FF FF 3F 00 00 00 3B 4C 38 01 ; Hidden boot part
      80 FE FF FF 07 FE FF FF 00 50 38 01 00 90 0A 24 ; Data
HDD2: 00 20 21 00 07 FE FF FF 00 08 00 00 00 48 38 3A ; Data + Backup

LBA 2 on original disk showing unwiped GRUB data

LBA 2 on HDD1

LBA 2047-2048 on 8 month old disk

LBA 2047-2048 on HDD2

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Please clarify. You show a windows boot record on #2048 of HD2, yet say that HD2 is not a boot drive, and the fragments of partition tables you show indicate likewise. – kreemoweet Sep 19 '12 at 17:54
@kreemoweet The partition is not bootable. Thats just what Windows puts in the boot sector of all NTFS partitions. – Cole Johnson Oct 6 '12 at 17:16
up vote 2 down vote accepted

You should be able to clear it out without issue since nothing should be using that anymore. However depending on your specific environment, you may end up having to reinstall the boot record, so keep your Windows disc handy to use the Recovery Options:

System Recovery

Just be careful about the range you wipe because there are parts of the file-system in those early sectors of a disk that appear empty but actually have a few bytes here and there (for example, keep an eye out for the signature (0x55 0xaa) which can appear a few times). Be extra careful about wiping the boot-sector (2048 in your case) when setting the range.

Also, are you using HxD to do the wiping? If so, you should note that you will not be able to do so from Windows 7 because as of Vista, direct/raw write-access to disks (especially to the system disk) is no longer allowed from programs without the use of a driver, which HxD does not use. You will need to either do it from another OS/live-CD or use a program that loads a driver.

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Your comment about HxD is incorrect. The restrictions on raw disk writing do not apply to disk sectors outside the file system, as this question concerns. – kreemoweet Sep 19 '12 at 17:39
About HxD, I thought HxD uses a libATA that communicates directly to the SATA without the OS. Also direct drive writes work with HxD on flash drives (that's all I've tested) – Cole Johnson Sep 19 '12 at 18:52
Unless they released a new version (alpha?) that supports it (which they have not), then no, HxD does not support raw-disk access in Vista+ yet. Note, they specifically says it will do so in the future and that a version that does is not out yet. And yes, it does indeed apply to the whole disk. Just last night I tried to write NULLs to several sectors of a FAT32 disk on a separate drive and could not. – Synetech Sep 19 '12 at 20:17

Yes, unless some app (such as an OEM recovery feature) is using those sectors. The same would apply to LBA 1 (LBA's start from 0, which is the MBR of the disk).

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GRUB code starts at LBA 2, so I know nothing is after the MBR – Cole Johnson Sep 19 '12 at 18:49

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