S-corp in IN but doing business in IL
In your case, you have two primary options to consider:
The first option, you could dissolve the S-Corporation in Indiana and open a new entity in Illinois. This would have the company registered in only one state, however, this would create a new date of formation for the business, as well as require a new federal tax id (EIN), S-Corp election, etc.
The second option, you can file your Indiana S-Corporation as a foreign entity in Illinois, which would have the business actively registered in both states, retaining the original date of formation and federal tax id.