Modified files will get overwritten with updated ones when you update the devkit. The launcher will tell you though that it copies everything modified to a backup. I’m not sure specifically where that is.
As for the grey objects, they have an error with their materials. See my thread about a workaround.
Most likely though this isn’t actually a problem outside of the editor. I wouldn’t worry about it unless you are taking screenshots in editor or unless you get the grey textures in game as well.