The file that I used to change my HUD colors is called GraphicsConfigurationOverride and is an XML document - there's no dot (.) in the file name. All mine has in it are the HUD colors.
It's a long time since I did this, and I backed up the original which has many other settings that are not in the live file.
The file for the HUD colors is in AppData>Local>Frontier Developments>Elite Dangerous>Options>Graphics
Edit - The original file is / was in a different location AppData>Local>Frontier_Developments>Products>elite-dangerous-64