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I don't think so. I haven't heard of it being a problem and boot camp isn't just software, it uses the firmware in your Mac, which is why you can't use boot camp on a hackintosh, but this means that it knows to look for the boot camp stuff first. I think it keeps it on a tiny hidden partition on your hard drive, IIRC, which messing about with Windows wouldn't affect.
Is any of this a legit issue on standard bootcamp? Mine's been perfectly behaved for the last 3 years and knowing that I potentially shouldn't trust it is annoying.