Don't worry, you cannot make any mistakes worse than the previous bookkeeper of improperly recording loan payments.
Without seeing how these payments were handled, if they were even paid back with business funds or personal funds it is impossible to tell if you have a pending tax consequence. You just missed the window to amend the 2016 tax return 2 days ago so all you can do is move forward.
Good news is payback of principal is not a taxable event although you may have missed getting a deduction for interest paid.
At this point I would use a journal entry to debit the loan account and credit owner equity
