The original loan would have been recorded as "Loans from Shareholders" on the Liability section of the balance sheet (the offset would be Cash).
The repayment on the loan would have reduced the liability balance (and also the cash account).
Since the tax return reported the ending balances of all balance sheet accounts, the "Loans from Shareholders" account would be the remaining balance on the loan.
None of these were taxable transactions, so there is no need to amend a prior year return. Simply report the current balance of the loan on your current balance sheet. You will most likely need to record some adjustment to equity in order to bring the balance sheet into balance.
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