Incorrect allocation of income between states

I am full-time resident of IL, but have WI income from LLC.

Also have capital gains that should be considered IL income.

Prepared IL state return first, then WI 1NPR. A large portion of the capital gains were allocated to WI.

I've read in other (similar, but different scenarios) answers that this may be caused by doing the "home" state return first, then the NR state. 

Does this mean I need to delete the state returns and redo, preparing WI first, then IL? Or is there another way?