Personally, I wouldn't trust them to not break things myself. I know they may not be "amateurs" at low level things like they do to make this happen, but I still wouldn't trust it. This is why my suggestion would be to use some kind of disk/filesystem encryption. TrueCrypt should be able to defeat them putting it back on and allow you to restore (from a clean copy) the original files and get your CHKDSK back.

On another note, I don't think I'd have ever noticed this myself, every laptop I've had I end up installing Linux on because of all the crapware that gets included with the OS in the first place.