You can't overwrite system files with NTLite, DISM or Sysprep. And btw, wimlib is available for windows.
Nuhi: Maybe it would be an usefull touch to give a pop-up message about permissions after you click open directory. Tell the user you need permission if you wanna modify something and maybe an external problem for easier process. (Nsudo for example)Right-click loaded image and choose Explore Mount Directory.
From there on it's the same as on installed Windows, files are not used so it's simpler, just need to take ownership before replacing or use tools like Unlocker.
At the end make sure to not have Explorer or any other opened tool using files or folders from the mount directory, then unload the image with saving, or Apply + save, to store the files into the actual image and unload the mount directory.