Windows (Vista, 7 & 8, anyway) usually tries to make a separate partition for booting. And when it does, it's almost always invisible to normal Windows stuff like the file manager.
Typically, this Windows boot partition is 100MEG, has a volume name called "System Reserved" and is NOT given a drive letter. Of course, you can still install Windows into one partition and not go this route, but you do have to go out of your way when installing Windows to do it.
So take another look at your drive partitioning using something like diskmgmt.msc (type that into your Windows start orb search pane to use the utility) to see if you don't have the 100Meg "System Reserved" partition. It's a little pointless but I just want to show that you probably have 2 partitions with Windows - not one.
Either way, we're really talking about a boot manager here. And if Grub does make a mistake then about all that will happen is that you might not be able to boot to Windows. But all your stuff should still be safe - and even accessible. It's still quite repairable but obviously a bit of a PITA too. (About the only "easy" way I've found to fix this sort of problem is to format the boot partition or intentionally screw up the boot flag or something like that and then let the Windows system recovery on DVD fix it).
So the short answer that Grub will overwrite stuff is not really possible or even an issue. Of course, if you have a failing hard drive where the SMART flag has been tripped or even if the data is seriously fragmented then that's another matter. Just don't go making it worse by adjusting partitions or especially formatting them.
And speaking of which... I hope you are defragmenting your Windows partition(s) under it's own power before using a Linux tool like GParted. Not defragging before shrinking a partition or adjusting it in any way is likely going to introduce a whole new set of problems. (So you can't say I didn't warn you.)