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:
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 U¬
(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.