You state this is a refinance of a real estate loan. You only have loan acquisition costs that are amortized and deducted over the life of the loan. You do not have any deductible real estate acquisition costs, because you can not acquire real estate that you already own.
If you change the cost basis of any asset listed in the assets/depreciation section of the SCH E, three things will happen.
1) The record of all prior year's deprecaition already taken will be changed by the program and therefore it will be wrong.
2) The current year's depreciation will be wrong
3) All future year's depreciation will be wrong.
All of that will come back to bite you in the tax year you sell or otherwise dispose of the property.
