I never had it mess up anything just by doing the Live CD.
I have had Linux flavors of Live CD's that load from CD when Windows disk fails. Meaning, I have had XP, Vista, & 7 machines, all 3 of those on different machines that people brought to me that would each fail to load to a disk prompt, or boot from the CD/DVD so you can do a repair.
Ultimate Boot CD would not load (Blue screen). If I am correct, windows uses a registry for most system settings while Linux is free from that method of data retention. Was able to view, see the files on the drive when all forms of windows based boot loaders failed. I am not 100% certain if this was a registry problem, bad driver problem, or what just yet. Perhaps it could be a lack of the right sata drivers on certain machines, or the hardware configurations used.
I was able to fix the machines, but I would sometimes (horrors?) have to use a combo 95/98se upgrade/me upgrade all in one disk with scandisk/format etc to delete the partition & then I could use XP/Vista/7 etc to set windows back up.
The reason I had to use it in some cases, is especially in cases where they do not care if you back up their data because they don't have important music/docs/games etc to backup, then it is faster to just use dos to do what all 3 other disks would fail to do.
I have bootable XP, Vista, 7 disks, & on some machines, not any of them could load to a place you can perform repairs or type commands because it would blue screen when it got to a certain part in the load process. I have noted that sometimes on laptops with certain kinds of sata drives, regular AHCI mode would blue screen. I will test later to see if it is a missing sata driver issue, but for now, I know others on the web have those problems in forums, & it can be worked around fairly easily usually by setting the drive to compatibility mode for the drive in the bios.
I was concerned that this may impact performance, but upon checking after load into windows, it seemed to run at normal DMA 5 or 6 mode with no problems. My understanding is AHCI is supposed to relieve a slight burden off the CPU, increasing the performance, but when I tested, the gain was so minimal that it wasn't noticed at all.
Peppermint/Ubuntu etc are really good for seeing what files are in windows, or perhaps even formatting the drive. Of course, using a 98 utility called fdisk can work as well. 98/me won't format as large of a drive as newer versions of windows, but they won't blue screen getting to your CD to run the harddisk partition tool either. In fact, you can just fdisk with 98, reboot, then use the XP/Vista/7 partition & install like normal.
I thought this would be interesting for you all to read.