If you replace all the files with the newer ones, the files that get replaced will be immediately deleted. You can't recover the files that have been replaced.
But if you manually deleted the game, go check the recycle bin and just restore everything that you had deleted.
I updated the game by Extracting the files right into the old files, but my saved files are still intact for some reason. Other people say that your save will be gone if you update the game that way, so people often recommend to other people to just make a Save Backup first before they do anything just in case something goes wrong.