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Well, the easy answer is that it shouldn't, but if you want to be absolutely sure it isn't affected you can always physically disconnect the drive first, and then reconnect it afterwards.
It should also be backed up to an external drive as further insurance.
You say you want to do a factory restore. Have you considered a clean install to get rid of all the garbage these manufacturer's load on your computer?
Check this tutorial, which explains how. Clean Reinstall - Factory OEM Windows 7