If you used the auto-overclock settings and haven't done any manual changes, you might as well try it and see. If they do change, just run the auto-overclock again and it should return you to your "normal" overclocked settings. The most you would have to do is reset the BIOS to defaults and run the auto-overclock again.
Most likely, the parameters are completely different between the different modes so it would override everything every time you switch. But that's just an educated guess.