Is there a file being created in your mod's RootTemplate folder after saving? The creation of the file is what indicates that your RootTemplate overwriting should be working. In general, the file won't be created the first time you try to save (and it throws the error) while it should be the second time.
If the file isn't being created then that would cause the game to revert back to the original upon loading the mod. If it is being created successfully, try saving again after making the changes one more time and see if it sticks.
