Just because you cannot update the extension information once the extension is filed does not mean that you cannot update information on your 1120S Form. Some of the information that you will not be able to change would be the name of the S-Corp and the EIN. Information related to the capital stock, balance sheet and profit and loss statements can be changed all the way up to when you actually file your 1120.
Therefore, you will simply make the changes and file normally by the extended due date.
