Since you used the wrong cost basis for 2 or more years for depreciation, amending is not an option. Per IRS Publication 946 at https://www.irs.gov/pub/irs-pdf/p946.pdf on page 14:
The following are examples of a change in method of accounting for depreciation.
• A change from an impermissible method of determining depreciation for depreciable property if the impermissible method was used in two or more consecutively filed tax returns.
So the IRS Form 3115 would need to be used. This form is not simple by any stretch of the imagination, and I highly urge you to seek professional help. This is especially true if your state also taxes personal income.
