You are referring to two separate years: If you have the balance sheet segment of a 2016 amended 1120S, the ending balances of  the 2016 amended return become the opening balances of the 2017 Form 1120S. What is perplexing, though is why a tax preparer would amend a balance sheet item on an  amended return, when they could do the same thing on a current years return as a prior period adjustment. I would look at the amended return, and you might discover that the change would have applied to an income/expense item, and not a balance sheet item. All you then do is close out the amended net income to retained earnings, and you are good to go forward.