This solution required 2 memory cards. one without any sc3 data on it(clean), and one with the corrupt data(corrupt).

-Put the memory card(corrupt).

-Turn on your ps2.

-Let it auto-load.

-Go to the memory card option and turn off the auto save.

-Remove the memory card(corrupt) and insert the memory card(clean) in slot 1.

-Start a new CotS game, go through the tutorial and die(fastest way to get to save).

-Save to the clean memory card.

-Exit to the SC3 title screen.

-Remove the clean memory card and put in the corrupt one.

-Goto Options and load your SC3 data.

-Remove the corrupt memory card and put in the clean one.

-Go back to CotS, load your game, die and save again.

-Solution is solved.