You are correct, you can deduct the unamortized costs in the year you dispose of the mortgage. You can go back three years and amend returns, but it may be more trouble and expense than it is worth.
Another option is to catch-up the missed amortization in the current year by filing form 3115. You can see this article on how do do this:
https://ttlc.intuit.com/community/amend-tax-return/help/what-should-i-do-if-i-didn-t-take-depreciati...
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