Let me first say that I have not had an opportunity to investigate this bug for myself.
However, my understanding is that BIOS writes a copy of itself to the uppermost LBAs of the drive, and then hides this image by reducing the capacity of the drive by a corresponding amount.
This article explains the Host Protected Area:
http://en.wikipedia.org/wiki/Host_protected_areaI don't know how or when the BIOS decides to do the above, but I presume that your affected drive was somehow promoted to the first device in the boot order. Either you did this intentionally, or maybe the first drive disappeared as a consequence of some fault.
Removing the HPA should not damage your file system. However, if the BIOS did manage to write to the drive, then the BIOS image must now be somewhere within the user area. I would use a disc editor to examine some likely locations.
HxD - Freeware Hex Editor and Disk Editor:
http://mh-nexus.de/en/hxd/For example, I would first examine the very last LBA on the drive. AIUI, in an NTFS volume this sector should contain a copy of the NTFS boot sector. Alternatively, depending on the OS, this copy may be in the middle of the volume. I'm assuming that partitions don't end on cylinder boundaries, in which case the above may not apply. In any case, you should be able to recognise BIOS code because the tail end of the image (last 16 bytes) will contain some uncompressed boot code, including a plain text BIOS ID.
BTW, the specs for your motherboard confirm the existance of an Xpress Recovery BIOS:
http://www.gigabyte.com.tw/Products/Mot ... GA-K8N-SLIThe latest BIOS version (F10E) is dated 2009/12/17:
http://www.gigabyte.com.tw/Support/Moth ... uctID=1928Here are some text strings I have extracted from the K8NSLI.10E image file in the above distribution:
"Award BootBlock BIOS v1.0"
"Can not Find BIOS Image in Hard Drive or Diskette"
"6A61FG0I"
You could scan your drive for the above strings.
If you find them, then you should determine which files, if any, occupy the affected sectors.
Tip: How to determine which file occupies a particular sector:
http://forums.seagate.com/t5/ATA-and-Se ... /m-p/35567