Regardless of weather you refi'd with the same lender or a different lender, if the amortized costs of the original loan are still being deducted over the life of that original loan, then leave well enough alone and continue to allow those costs to be deducted each year.
Otherwise if my above assumption is wrong, then as you stated, amended the 2016 tax return will not change anything. You'll just have to accept the loss unfortunately.
