It only affects the install files for the actual game. It doesn't make any changes to save game files. If you have any mods in the game, you may need to remove those first before running the repair tool.
Essentially, it compares your installed game files with the files on the Origin server and re-downloads any files that are different. It will also repair registry entries for the game if any have been altered or erased.
Hope this helps and happy Simming!
Flynn