They're both okay, but they mean different things.
The first one means "it" could change and that "that" isn't necessarily what "it" is. E.g. "The doctors think she has a cold, but if it's anything other than that, she may have to take medicine." ("It" is her illness - whatever it is; "that" is her having a cold.)
The second one means that there could be more than just "that". E.g. "I can't help you make the cake, but if there's anything other than that I can help you with, just let me know." ("That" refers to baking the cake.)