I know it may sound odd. I have an original copy of counter strike in my steam. But I like a non steam mod of cs . I intend to copy over original files. So which files I shouldnt replace to keep it original steam game?
The game is not original anymore when you replace anything but the save files. I would suggest you to make a backup and then simply copy over what you need to in order to install your mod.
You have to ask yourself what if your goal in keeping the game an "original steam game". If it is functionality, then the mod - if it is properly written, should keep it working. If it is more an intellectual question such as for copyright or "this is the original version" type of questions, you should not change anything at all.
In general, making a backup of the files should be a standard procedure - unless you are fine with deleting everything and re-downloading it.