I doubt you are not applying for any intelligence agencies 
You can get out a colour copy with a duplicate (or Not Original) mark on it. Most good copiers do that themselves (go to water pump). There is nothing wrong in that if your employer if a color freak.
Father's CNIC and the CNICs of references produced at interview are required by sensitive organizations occasionally as a pre-recruitment protocol. If you are going to give them such, do mark and cross them for only specific use on both sides.
If your employer is a one which provides over seas employment than this might be quite a normal case for possible future scams 
By the way I'm a amused that they actually asked for your father's CNIC lolz 