I'm not sure how that would cause an issue. I use Putty as well. It's really just a terminal application so it should have nothing to do with how Linux operates. If you save the file, close it, then open it again it should be as saved. If not, that's a problem. You could also try logging off and then back on with Putty to verify. I'm not sure what would cause Linux to replace files after reboot so it really has to be a problem writing the files IMO.