It will only replace missing or altered files. Backup your ini files just in case. Also backup any vanilla bsa's and esm's that you cleaned, and copy them back in when Steam is finished doing it's thing. Or, before running Steam, just copy the originals back in if you already backed them up, so you don't have to redownload. It won't mess with any files you added through modding. You can backup the entire folder if you are paranoid ;)