The way it should have been done was to enter the building as non-residential real estate, which would result in a 39 year depreciation period. Then, when you refinanced, fees associated with the refinance should be amortized separately over the remaining period of the loan.
I think what you mean is you combined the original cost of the the building somehow with the finance costs and started amortizing the new basis over 39 years? If so, then your deduction would be about the right amount, but would appear as amortization expense on the tax return as opposed to depreciation expense.
The two are similar but not technically the same. If you got audited, you could amend the returns for the last three years but beyond that the IRS may disallow the amortization expense and not allow the associated depreciation since you didn't report it properly.
For purposes of reporting the sale, you need to recognize the depreciation that should have been taken even if you didn't take it, but your asset basis in TurboTax would be close to what it should be, so when you report the sale your gain should be close to what it should be as well.
The best solution would be to delete the asset and reenter it as two items, the building and finance fees. You amortize the finance fees over the term of the mortgage and the building gets depreciated based on what type of asset you designate it to be. When you enter the date put into service, TurboTax will calculate the prior and current year depreciation, so your sale will be properly recorded.
To amend the prior year returns would involve a lot of work, so if the depreciation expense was not material, it may be more work than you want to fool with, especially since the tax won't change much.
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